From rhubley@systemsbiology.org Thu Nov 6 14:38:31 2003 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id hA6McVA5001166 for ; Thu, 6 Nov 2003 14:38:31 -0800 Received: from [198.107.152.39] (HELO systemsbiology.org) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 3689422 for rmannounce@repeatmasker.org; Thu, 06 Nov 2003 14:36:49 -0800 Message-ID: <3FAACD01.7010207@systemsbiology.org> Date: Thu, 06 Nov 2003 14:36:49 -0800 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Rmannounce] testing X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 06 Nov 2003 22:38:31 -0000 testing -- "A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death." - Martin Luther King From rhubley@systemsbiology.org Thu Nov 6 14:44:54 2003 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id hA6MisA5001199 for ; Thu, 6 Nov 2003 14:44:54 -0800 Received: from [198.107.152.39] (HELO systemsbiology.org) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 3689447 for rmannounce@repeatmasker.org; Thu, 06 Nov 2003 14:43:12 -0800 Message-ID: <3FAACE80.2070500@systemsbiology.org> Date: Thu, 06 Nov 2003 14:43:12 -0800 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Rmannounce] help also X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 06 Nov 2003 22:44:54 -0000 help also -- "A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death." - Martin Luther King From rhubley@systemsbiology.org Wed Sep 1 10:52:33 2004 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id i81HqXJr027947 for ; Wed, 1 Sep 2004 10:52:33 -0700 Received: from [198.107.152.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 4526100 for rmannounce@repeatmasker.org; Wed, 01 Sep 2004 10:47:44 -0700 Message-ID: <41360B3B.40306@systemsbiology.org> Date: Wed, 01 Sep 2004 10:47:39 -0700 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: multipart/alternative; boundary="------------040107020004000009080800" Subject: [Rmannounce] RepeatMasker News X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 01 Sep 2004 17:52:33 -0000 This is a multi-part message in MIME format. --------------040107020004000009080800 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit *New Pre-Masked Genomes Page* With the help of UCSC's bio-computing cluster and the RepeatMasker program we have assembled a database of repeat annotations for several draft genomes. Currently we have annotations for the latest Rat, Mouse and Human assemblies. The database may be queried from the "Pre-Masked Genomes " page using a variety of filter, and formatting options. *RepeatMasker in transition* RepeatMasker is becoming open source! A new version "open-3.0" will be out soon. Many new features including full integration with WUBlast, simplified installation scripts, and a new species selection interface have been added. If you would like to be notified when the new release is available click here . -- "A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death." - Martin Luther King --------------040107020004000009080800 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

New Pre-Masked Genomes Page
With the help of UCSC's bio-computing cluster and the RepeatMasker program we have assembled a database of repeat annotations for several draft genomes. Currently we have annotations for the latest Rat, Mouse and Human assemblies. The database may be queried from the "Pre-Masked Genomes" page using a variety of filter, and formatting options.
RepeatMasker in transition
RepeatMasker is becoming open source! A new version "open-3.0" will be out soon. Many new features including full integration with WUBlast, simplified installation scripts, and a new species selection interface have been added. If you would like to be notified when the new release is available click here. 



-- 


"A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death."

- Martin Luther King
--------------040107020004000009080800-- From rhubley@systemsbiology.org Wed Sep 15 16:05:04 2004 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id i8FN54Jr008525 for ; Wed, 15 Sep 2004 16:05:04 -0700 Received: from [198.107.152.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 4564164 for rmannounce@repeatmasker.systemsbiology.net; Wed, 15 Sep 2004 15:59:03 -0700 Message-ID: <4148C92E.5050704@systemsbiology.org> Date: Wed, 15 Sep 2004 15:58:54 -0700 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.systemsbiology.net Content-Type: multipart/alternative; boundary="------------000507070208070106060300" Cc: Subject: [Rmannounce] RepeatMasker Open-3.0 Released X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 15 Sep 2004 23:05:05 -0000 This is a multi-part message in MIME format. --------------000507070208070106060300 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit *RepeatMasker open-3.0 Released* RepeatMasker open-3.0 is now available for download. Thanks to the University of Washington Digital Ventures Group and the Institute for Systems Biology the program is now licensed under the Open Source License v2.1 . New features in this release include: * *DateRepeats Script* - Resolves which repeats are likely to i predate the speciation of two or more species. * *Native WUBlast Integration* - The WUBlast sequence search engine can be used with RepeatMasker without the need of the MaskerAid package. * *Taxonomy Database* - The NCBI Taxonomy database is now used for species specification. * *Library Caching* - Species specific libraries are created and cached on the fly. Two levels of caching ( system and user ) allow an admistrator to manage where files are stored. * *Install Script* - A new install script makes it easier to install and configure RepeatMasker. * *New Utilities* - Two utilities are included to assist in querying the repeat consensus and taxonomy databases. To request the new release click here . -- "A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death." - Martin Luther King --------------000507070208070106060300 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit RepeatMasker open-3.0 Released
RepeatMasker open-3.0 is now available for download. Thanks to the University of Washington Digital Ventures Group and the Institute for Systems Biology the program is now licensed under the Open Source License v2.1. New features in this release include:
  • DateRepeats Script - Resolves which repeats are likely to i predate the speciation of two or more species.
  • Native WUBlast Integration - The WUBlast sequence search engine can be used with RepeatMasker without the need of the MaskerAid package.
  • Taxonomy Database - The NCBI Taxonomy database is now used for species specification.
  • Library Caching - Species specific libraries are created and cached on the fly. Two levels of caching ( system and user ) allow an admistrator to manage where files are stored.
  • Install Script - A new install script makes it easier to install and configure RepeatMasker.
  • New Utilities - Two utilities are included to assist in querying the repeat consensus and taxonomy databases.
To request the new release click here. 
-- 


"A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death."

- Martin Luther King
--------------000507070208070106060300-- From rhubley@systemsbiology.org Tue Sep 28 15:51:55 2004 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id i8SMpsJr026204 for ; Tue, 28 Sep 2004 15:51:54 -0700 Received: from [198.107.152.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 4623295 for rmannounce@repeatmasker.systemsbiology.net; Tue, 28 Sep 2004 15:44:47 -0700 Message-ID: <4159E956.7030804@systemsbiology.org> Date: Tue, 28 Sep 2004 15:44:38 -0700 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla Thunderbird 0.8 (X11/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.systemsbiology.net Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Cc: Subject: [Rmannounce] WUBlast "out of memory" bugfix X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 28 Sep 2004 22:51:55 -0000 A bugfix is available for RepeatMasker open-3.0 which corrects a problem with short sequences run with the WUBlast option. If a search is performed on a large sequence file containing many short ( less than 100bp sequences ) *and* during batching one of these sequences ends up being placed as the last entry in a particular batch you may see the following error messages: identifying full-length ALUs in batch # of # ERROR from search engine (16) retrying comparison with smaller bandwidth This is not a memory problem, rather a problem with the way we handled exceptions returned by WUBlast. The fix is to replace the WUBlastSearchEngine.pm file in your RepeatMasker installation directory with the new version available here: http://www.repeatmasker.org/WUBlastSearchEngine.pm From rhubley@systemsbiology.org Tue Feb 22 11:24:34 2005 Received: from systemsbiology.org (mail.systemsbiology.net [198.107.152.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id j1MJOYXO006664 for ; Tue, 22 Feb 2005 11:24:34 -0800 Received: from [198.107.152.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 5088114 for rmannounce@repeatmasker.org; Tue, 22 Feb 2005 11:20:54 -0800 Message-ID: <421B8611.7090605@systemsbiology.org> Date: Tue, 22 Feb 2005 11:20:49 -0800 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla Thunderbird 0.9 (X11/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [Rmannounce] WUBlast & Custom Libraries X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 Feb 2005 19:24:35 -0000 A bug has been found which effects all open-3.x releases. If you use a custom database ( as in "-lib mylib.fa" ) with the WUBlast search engine you will only get the forward strand matches to your repeat library. Also as some of you have noted you will also have to create the WUBlast frozen libraries manually. A new release of RepeatMasker is in the works which will correct both of these problems. In the meantime the following workaround will work with all open-3.x releases: 1. *Add reverse strand sequences to your library:* * For each sequence in your custom library create a reverse complemented copy of the sequence. i.e >REP1 A novel repeat AACCAGTC becomes: >REP1 A novel repeat GACTGGTT * Name the reverse complemented copy with the same id and description plus the suffix " (anti)". i.e >REP1 A novel repeat (anti) GACTGGTT * Combine the original and reverse complemented sequences into one fasta file. i.e >REP1 A novel repeat AACCAGTC >REP1 A novel repeat (anti) GACTGGTT 2. *Create a WUBlast database out of your library:* * Locate the wublast setdb program. This is usually found in the WUBlast program directory. * Run the program as "setdb mylib.fa". 3. *Run RepeatMasker* - You should now be able to run RepeatMasker with the options: RepeatMasker -w -lib mylib.fa sequencefile.fa From rhubley@systemsbiology.org Mon May 2 15:46:52 2005 Received: from systemsbiology.org (mail.systemsbiology.net [209.124.189.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id j42MkqG4014312 for ; Mon, 2 May 2005 15:46:52 -0700 Received: from [209.124.189.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 5337697 for rmannounce@repeatmasker.org; Mon, 02 May 2005 15:46:51 -0700 Message-ID: <4276ADD2.6050603@systemsbiology.org> Date: Mon, 02 May 2005 15:46:42 -0700 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla Thunderbird 0.9 (X11/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [Rmannounce] RepeatMasker: New Repeat Protein Masking Webservice X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 02 May 2005 22:46:52 -0000 A new webservice has been added which compares DNA sequences to a database of transposable element encoded proteins. The service masks the input sequence and provides a table of annotations. You can try the webservice here: http://www.repeatmasker.org/RepeatProteinMaskRequest. Note that copies of non-coding transposable elements like SINEs and long terminal repeats of retroviral-like elements will not be masked and the masked sequence is not "ready" for DNA based comparisons. However, this approach is especially useful when no repeat library is yet available for the query species and the primary concern is avoiding spurious matches in BLASTX-like searches. The method is also much faster than the DNA based approach. False positives are minimal but be aware of the existence of transposable element derived genes. From rhubley@systemsbiology.org Tue May 3 12:40:41 2005 Received: from systemsbiology.org (mail.systemsbiology.net [209.124.189.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id j43JefG4016207 for ; Tue, 3 May 2005 12:40:41 -0700 Received: from [209.124.189.39] (HELO [10.0.1.88]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 5341094 for rmannounce@repeatmasker.org; Tue, 03 May 2005 12:40:41 -0700 Message-ID: <4277D3B2.3050809@systemsbiology.org> Date: Tue, 03 May 2005 12:40:34 -0700 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Mozilla Thunderbird 0.9 (X11/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [Rmannounce] RepeatMasker open-3.1.0 update released X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 03 May 2005 19:40:41 -0000 RepeatMasker open-3.1.0 is available for download here: http://www.repeatmasker.org/RMDownload.html This release includes several bug fixes: * *WU-Blast & Custom Libraries* - RepeatMasker now handles searching the reverse strand correctly when supplied with a custom library via the "-lib" parameter. * *DeCypher Search Engine* - TimeLogic has contributed a module to the RepeatMasker project which adds support for their DyCypher search engine. From rhubley@systemsbiology.org Wed Nov 2 13:59:18 2005 Received: from systemsbiology.org (mail.systemsbiology.net [209.124.189.58]) by repeatmasker.systemsbiology.net (8.12.8/8.12.8) with SMTP id jA2LxIwH029540 for ; Wed, 2 Nov 2005 13:59:18 -0800 Received: from [209.124.189.39] (HELO [10.0.5.95]) by systemsbiology.org (CommuniGate Pro SMTP 4.0.5) with ESMTP id 6000318 for rmannounce@repeatmasker.org; Wed, 02 Nov 2005 13:59:18 -0800 Message-ID: <436936AF.2050809@systemsbiology.org> Date: Wed, 02 Nov 2005 13:59:11 -0800 From: Robert Hubley Organization: Institute for Systems Biology User-Agent: Thunderbird 1.4 (X11/20050908) MIME-Version: 1.0 To: rmannounce@repeatmasker.org Content-Type: multipart/alternative; boundary="------------000402080906050008090909" Subject: [Rmannounce] RepeatMasker open-3.1.2 released X-BeenThere: rmannounce@repeatmasker.org X-Mailman-Version: 2.1.3 Precedence: list List-Id: RepeatMasker Announcements Mailing List List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 02 Nov 2005 21:59:19 -0000 This is a multi-part message in MIME format. --------------000402080906050008090909 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit RepeatMasker open-3.1.2 is available for download: www.repeatmasker.org/RMDownload.html This release includes the following changes: * *Library Updates* - The databases have grown considerably again, with a new opossum library and several extensions made by GIRI, including a preliminary sea urchin library. These are the numbers for a few better represented species: species # of consensi total bp Mammalian-wide 339 472647 Primates * 401 686251 * Excluding mammalian-wide elements Rodents * 462 717119 Carnivores * 101 149290 Marsupials * 105 162839 Chicken 92 177063 Fugu (pufferfish) 95 175420 Danio (zebrafish) 214 459777 Ciona (two sea squirts) 127 304646 Strongylocentrotus 86 124328 Drosophila 214 611814 Anopheles 280 721533 Caenorhabditis (2 spec) 354 525523 Arabidopsis 457 1460558 Oryza (rice) 525 1154651 Wheats (Triticeae) 198 494718 Zea (maize) 65 206724 Thalassiosira diatom 40 96637 Chlamydomonas algae 65 137363 * *Library Format Changes* - A new EMBL-like format for RepeatMasker's main library file adds expanded annotations to the repeat library. Repbase ID aliases are now noted in this file where applicable. Custom library input format hasn't changed. * *Fail Early Behavior* - RepeatMasker now reports unrecoverable search errors early rather than at the end of batch processing. This applies to users who use the parallel( -pa ) options and had to wait an extended period of time to learn that the first search failed. --------------000402080906050008090909 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit RepeatMasker open-3.1.2 is available for download: www.repeatmasker.org/RMDownload.html
This release includes the following changes:
  • Library Updates - The databases have grown considerably again, with a new opossum library and several extensions made by GIRI, including a preliminary sea urchin library.
These are the numbers for a few better represented species:

species         # of consensi  total bp
Mammalian-wide          339    472647
Primates *              401    686251  * Excluding mammalian-wide elements
Rodents *               462    717119
Carnivores *            101    149290
Marsupials *            105    162839
Chicken                  92    177063
Fugu (pufferfish)        95    175420
Danio (zebrafish)       214    459777
Ciona (two sea squirts) 127    304646
Strongylocentrotus       86    124328
Drosophila              214    611814
Anopheles               280    721533
Caenorhabditis (2 spec) 354    525523
Arabidopsis             457   1460558
Oryza (rice)            525   1154651
Wheats (Triticeae)      198    494718
Zea (maize)              65    206724
Thalassiosira diatom     40     96637
Chlamydomonas algae      65    137363
  • Library Format Changes - A new EMBL-like format for RepeatMasker's main library file adds expanded annotations to the repeat library. Repbase ID aliases are now noted in this file where applicable. Custom library input format hasn't changed.
  • Fail Early Behavior - RepeatMasker now reports unrecoverable search errors early rather than at the end of batch processing. This applies to users who use the parallel( -pa ) options and had to wait an extended period of time to learn that the first search failed. 




--------------000402080906050008090909--

From rhubley@systemsbiology.org Mon Dec  5 17:04:09 2005
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Subject: [Rmannounce] RepeatMasker Webserver Back Online
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**

    *

    *The RepeatMasker webserver lost a disk over the weekend.
    We apologize for any inconvenience this may have caused. The system
    is now back online and available for use. We will be upgrading the
    webserver in the near future so that disk failures will not remove the
    system from service.  Thanks for your patience.




-- 
Creationists make it sound as though a 'theory' is something you dreamt up after being drunk all night - Carl Sagan (1934 - 1996)

Look!!
I just want sharks with frikken laserbeams attached to their heads!



From rhubley@systemsbiology.org Fri Jan 20 14:54:07 2006
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Subject: [Rmannounce] RepeatMasker Open-3.1.3 Released
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  **

    RepeatMasker open-3.1.3 is available for download at
    http://www.repeatmasker.org/RMDownload.html
    . This release includes
    the following changes:

        * *Marsupial Masking* - Changes have been made to the library
          and the program which improve the masking of marsupial genomes.
        * *Library Updates* - The database has been synched with Repbase
          version 10.11. The new library is available at GIRI as
          repeatmaskerlibraries-20060120.tar.gz.
        * *Cache Fix* - RepeatMasker was building and rebuilding cached
          libraries for species where no species-specific repeat
          libraries existed. This behaviour was corrected.


From rhubley@systemsbiology.org Tue Feb 21 11:29:51 2006
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The RepeatMasker compute cluster and website will be down Thursday February
23rd and Sunday February 26th for upgrades and preventative 
maintenance.  We
apologize for the inconvenience.  Please do not submit large jobs on 
Wednesday or
Saturday as they may have to be canceled when the machines are shutdown.



From rhubley@systemsbiology.org Wed Mar 15 15:12:46 2006
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     *RepeatMasker open-3.1.4 Released*

    RepeatMasker open-3.1.4 is available for download
    http://www.repeatmasker.org/RMDownload.html. This release includes
    the following changes:

        * *Reduced False Positives* - We have observed that false
          positives are often caused by stretches of simple repeats
          matching a low complexity block of an interspersed repeat.
          This new version of RepeatMasker employs a technique which
          reduces the chance that these types of matches are interpreted
          as interspersed repeats.
        * *Mouse/Rat Bug Fix* - RepeatMasker searches ran with the
          "-species rat" or "-species mouse" underperformed searches run
          with "-species rodentia". Thanks to Angie Hinrichs of UCSC for
          finding this one.
        * *Library Updates* - The database has been synched with Repbase
          version 11.01. The new library is available at GIRI 
           as
          repeatmaskerlibraries-20060314.tar.gz. Many new Marupial
          repeats have been added. In the near future we will release a
          comprehensive list of new and modified repeats for each
          database update.

*New Pre-Masked Genome Annotations Available*

    The November 2003 and the January 2006 assemblies of the chimp
    genome ( panTro1 and panTro2 ), the May 2005 assembly of the dog (
    canFam2 ), the May 2005 assembly of the Zebrafish genome ( danRer3
    ), and the August 2002 assembly of the takifugu genome ( fr1 ) have
    been added to the Pre-Masked Genomes Page
    . You can
    query RepeatMasker annotations, alignments, and masked sequence
    using this webservice. 


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       RepeatMasker open-3.1.4
Released  
    

    

      
      
 RepeatMasker open-3.1.4 is available for download
http://www.repeatmasker.org/RMDownload.html. This release includes the
following changes:
        
    
          
  • Reduced False Positives - We have observed that
false positives are often caused by stretches of simple repeats
matching a low complexity block of an interspersed repeat. This new
version of RepeatMasker employs a technique which reduces the chance
that these types of matches are interpreted as interspersed repeats. 
    • 
          
  • Mouse/Rat Bug Fix - RepeatMasker searches ran with
the "-species rat" or "-species mouse" underperformed searches run with
"-species rodentia". Thanks to Angie Hinrichs of UCSC for finding this
one. 
    • 
          
  • Library Updates - The database has been synched
with Repbase version 11.01. The new library is available at GIRI  as
repeatmaskerlibraries-20060314.tar.gz. Many new Marupial repeats have
been added. In the near future we will release a comprehensive list of
new and modified repeats for each database update. 
    • 
        

      

      		
    

  




  
    

        New Pre-Masked Genome
Annotations Available  
    

    

      
      
The November 2003 and the January 2006 assemblies of
the chimp genome (
panTro1 and panTro2 ), the May 2005 assembly of the dog ( canFam2 ),
the May 2005 assembly of the Zebrafish genome ( danRer3 ), and the
August 2002 assembly of the takifugu genome ( fr1 ) have been added to
the Pre-Masked
Genomes Page. You can query RepeatMasker annotations, alignments,
and masked sequence using this webservice. 

      		
    

  







--------------060101060906090902020802--

From rhubley@systemsbiology.org Mon Mar 20 15:36:09 2006
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Subject: [Rmannounce] Open-3-1-5 Released - Bug Fix for Non-Mammals
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  **Unfortunately a bug made it into our latest release of RepeatMasker 
and was not caught by our unit tests. This causes the species specific 
cached libraries to be incorrectly created for non-mammal species. 
RepeatMasker open-3.1.5 is available for download here: 
http://www.repeatmasker.org/RMDownload.html. If you have downloaded 
open-3.1.4 and are working with non-mammal species such as chicken 
please download this update immediately. Web server runs performed with 
open-3.1.4 for non-mammal species should also be re-run.

        * *Installation Note:* You may copy your existing library
          Libraries/RepeatMaskerLib.embl over to the new package. You
          should edit this file and change the release version ( line 10
          ) from:
          /CC RELEASE 20060314; /
          to
          /CC RELEASE 20060315;/
          If this is a first installation of the library than this
          change is not necessary.



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 Unfortunately
a bug made it into our latest release of RepeatMasker and was not
caught by our unit tests. This causes the species specific cached
libraries to be incorrectly created for non-mammal species.
RepeatMasker open-3.1.5 is available for download here:
http://www.repeatmasker.org/RMDownload.html. If you have downloaded
open-3.1.4 and are working with non-mammal species such as chicken
please download this update immediately. Web server runs performed with
open-3.1.4 for non-mammal species should also be re-run.


  
    
    
  • Installation Note: You may copy your existing library
Libraries/RepeatMaskerLib.embl over to the new package. You should edit
this file and change the release version ( line 10 ) from:
    
      CC RELEASE 20060314; 
    
to
    
      CC RELEASE 20060315;
    
If this is a first installation of the library than this change is not
necessary.
    • 
  

  








--------------060009020903040002030702--

From rhubley@systemsbiology.org Fri Oct  6 17:25:42 2006
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Subject: [Rmannounce] RepeatMasker open-3.1.6 Released
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**

    A new version of RepeatMasker is available for download
    . Included in this new
    release are several major improvements:

        * The repeat database is updated with 694 new entries and 147
          improvements on existing ones, including RepBase version
          11.06. Major advances were for ancient mammalian repeats,
          which are shared by all mammals or all eutherians, and for
          marsupial repeats, especially for the opossum. Other
          significant additions were for Chlamydomonas and
          Caenorhabditis briggsae.
        * The annotation of DNA Transposon fragments has been improved.
          A new method of joining related transposon fragments improves
          classification of ambiguous fragments. More details here
          
        * A new option ( -lcambig ) identifies DNA Transposon
          annotations which without any supporting evidence are
          ambiguously defined. i.e The fragment falls within a
          non-unique portion of the family consensus. When this option
          is used all ambiguous repeat names are printed in lower case
          while the rest are in uppercase.
        * Fixed a bug with fasta files containing more than 60MB of
          sequence on a single file line.
        * Updated the taxonomy database and added the "-tree" option to
          the queryRepeatDatabase.pl script. The new option prints out
          the taxonomic tree of all species contained in the
          RepeatMasker database with information on the number of repeat
          families defined at each level.
        * Several bugs have been fixed in the DateRepeats routine, which
          played when large numbers were involved (e.g. analysis of
          whole chromosome RepeatMasker output) and/or the input is a
          concatenation of RepeatMasker outputs (repeat IDs are not
          necessarily unique anymore).
        * Other improvements in DateRepeats are better labeling of
          ambiguously called repeats, correctly assignment of lineage
          specificity to some elements that have independently inserted
          in separate lineages of mammals, and refinements in the
          phylogeny.


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 A new version of RepeatMasker is available for download.
Included in this new release are several major improvements:
  
    
    
  • The repeat database is updated with 694 new entries and 147
improvements on existing ones, including RepBase version 11.06. Major
advances were for ancient mammalian repeats, which are shared by all
mammals or all eutherians, and for marsupial repeats, especially for
the opossum. Other significant additions were for Chlamydomonas and
Caenorhabditis briggsae. 
    • 
    
  • The annotation of DNA Transposon fragments has been improved. A
new method of joining related transposon fragments improves
classification of ambiguous fragments. More details here 
    • 
    
  • A new option ( -lcambig ) identifies DNA Transposon annotations
which without any supporting evidence are ambiguously defined. i.e The
fragment falls within a non-unique portion of the family consensus.
When this option is used all ambiguous repeat names are printed in
lower case while the rest are in uppercase. 
    • 
    
  • Fixed a bug with fasta files containing more than 60MB of
sequence on a single file line. 
    • 
    
  • Updated the taxonomy database and added the "-tree" option to
the queryRepeatDatabase.pl script. The new option prints out the
taxonomic tree of all species contained in the RepeatMasker database
with information on the number of repeat families defined at each
level. 
    • 
    
  • Several bugs have been fixed in the DateRepeats routine, which
played when large numbers were involved (e.g. analysis of whole
chromosome RepeatMasker output) and/or the input is a concatenation of
RepeatMasker outputs (repeat IDs are not necessarily unique anymore). 
    • 
    
  •  Other improvements in DateRepeats are better labeling of
ambiguously called repeats, correctly assignment of lineage specificity
to some elements that have independently inserted in separate lineages
of mammals, and refinements in the phylogeny. 
    • 
  








--------------030803060702020006000705--

From rhubley@systemsbiology.org Tue Apr 17 15:07:09 2007
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Subject: [Rmannounce] RepeatMasker Beta Release Available
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RepeatMasker Beta Release Available

    A new version of RepeatMasker ( Open-3-1-7 ) is available for
    testing at download .
    This version includes a major refactoring of the ProcessRepeats code
    along with many bugfixes. Due to the volume of changes in this
    release we are offering it as a downloadable beta-release for a
    short period while we continue to test it. The webserver will
    continue to use open-3-1-6 until we are ready for the official
    release. Changes in the release include:

        * Repeat Defragmentation Improvements: The defragmentation
          stages of ProcessRepeats have been refactored improving the
          annotation of LTR, LINE and SINE repeats.
        * Metadata Migration: We have begun to move metadata ( subfamily
          relationships, consensus model relationships, genomic
          frequency etc ) out of the ProcessRepeats code. In the near
          future this will provide researchers greater access to these
          detailed repeat characteristics and enable the same processing
          rules to be used on custom generated repeat libraries.
        * Bugfixes:
              o IS Element Bugfix: In certain cases the extraction of IS
                elements fails causing the sequences indices to be off.
                The final result is an error message of the form:
                "ArrayList::get( -1 ) Index out of bounds!".
              o Division By Zero Bugfix: Under special circumstances
                ProcessRepeats produces a "Illegal division by zero at
                ProcessRepeats line 1860." error.
              o Long Sequence Names Bugfix: Long sequence names > 20
                characters can cause ProcessRepeats to fail. Thanks to
                Gordon Lack for finding and reporting this.
              o Negative Sequence Positions Bugfix: ProcessRepeats was
                reporting negative sequence positions in the final
                output file.


From rhubley@systemsbiology.org Wed Apr 18 17:55:20 2007
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Subject: [Rmannounce] RepeatMasker Cluster Downtime Tomorrow
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The RepeatMasker cluster will be down tomorrow morning ( Thursday April 
19th ) at 8am for critical filesystem maintenance. Cluster jobs running 
at this time will be canceled.  We apologize for the short notice and 
the inconvenience. The cluster should be back online by midday.


From rhubley@systemsbiology.org Thu Apr 19 11:45:43 2007
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The maintenance work is complete.  The webserver is available for use. 

-R


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  *
*

    The recent beta version of RepeatMasker has been tested and is now
    ready for an official release. We assigned it the version
    "Open-3-1-8" as there were several minor bugs fixed. You may
    download the release from here: download
    . The webserver is now
    running the updated version as well. 


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A bug in ProcessRepeats causes the program to crash when rare transposon 
join scenarios are encountered. The error message looks like this: 
"join(): Invalid join!$this == $partner at ProcessRepeats line 8164." or 
this: "This violates recursion....Died at ProcessRepeats line 1828". The 
fix is to replace your Open-3.1.8 ProcessRepeats file with the one 
contained in this archive RepeatMasker-open-3-1-8-patch-1.tar.gz 
. 
NOTE: You may have to alter the first line in ProcessRepeats to 
correctly reference your perl installation location.

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Yesterday we experienced some problems with a disk drive on RepeatMasker 
webserver.  Jobs submitted yesterday may not have completed.   The 
problem has been fixed and the server has been restored to full 
capacity.  Unfortunately we cannot restore jobs submitted during the 
outage and must be resubmitted. 

We apologize for the inconvenience,

-R


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Subject: [Rmannounce] RepeatMasker Evidence Reporting
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RepeatMasker Evidence Reporting

   A new version of the RepeatMasker webservice has been installed. The 
new version produces an additional output file ( *.out.html ) which 
provides the evidence ( source hsps ) with each final annotation call. 
The page is displayed in the typical one-annotation-per-line format with 
links ( the "+" preceding each line ) to expand the evidence data below 
the line. In addition to evidence reporting the repeat names on this new 
page link to details for each particular type of repeat.


From rhubley@systemsbiology.org Fri Aug 10 11:17:10 2007
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We had an unexpected outage this morning due to some disk problems.  
While the server is back up now we may need to schedule another outage 
should the problems continue.

Thanks for your patience,

-R

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Subject: [Rmannounce] New RepeatMasker Libraries Available
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A new version of the RepeatMasker repeat library ( RMLib: 20071204,
RepBase: 12.06 ) is now available for download from GIRI (
www.girinst.org ).

-- 




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Subject: [Rmannounce] RepeatMasker Open-3-1-9 Released
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  **
RepeatMasker Open-3-1-9 Released


A new version of RepeatMasker is available for download ( 
http://www.repeatmasker.org/RMDownload.html ) . Updates include:

        * Codebase synced to recently released library RMLib 20071204.
        * Improved DNA transposon fragment identification.
        * BugFix: The .align files generated by 3.1.8 did not contain
          cross_match style headers for each alignment.
        * BugFix: ProcessRepeats will infrequently exit in cycle 10 with
          the error: /cycle 10 Can't call method "addDerivedFromAnnot"
          on an undefined value at ProcessRepeats line 3835./ No results
          for the search are given.

-- 




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Subject: [Rmannounce] DEBUG Messages 
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The latest release of RepeatMasker contained a few debugging statements 
turned on by mistake.  These are not errors and do not indicate a 
problem with your search.  The running output will look something like this:

Processing output:
cycle 1
cycle 2
cycle 3 After:
After:
After:
cycle 4
cycle 5
cycle 6
cycle 7 Naming Current:
 353 33.1 6.5 0.6 sequence1        2970     3139     6193 C L2a_3end#LINE/
L2       3088     3267      159   5   2
 --  353 33.1 6.5 0.6 sequence1        2970     3139     6193 C L2a_3end#L
INE/L2       3088     3267      159   5   2
   \--- ID=2 con{ID} =  highest =
...

To remove these you may either download the distribution again from our 
website or you may edit
the ProcessRepeats file:

Change line 7082:

From:
    print "After:\n";
To:
   #  print "After:\n";


Change line 2335

From:
   $DEBUG          = 1;
to:
   $DEBUG          = 0;


Sorry for the confusion,

-Robert


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Subject: [Rmannounce] New Compute Node & Scheduler
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The RepeatMasker cluster received a new compute node ( for processing 
web requests ) and an upgrade to the job scheduler over the weekend.  
This upgrade should improve the overall throughput of the masking 
service.  Please let us know if you have any problems submitting jobs or 
receiving your results.

Thanks,

-R


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Subject: [Rmannounce] RepeatMasker Cluster etc...
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Unexpected Downtime:

At 3am last night the RepeatMasker cluster went down unexpectedly. We 
restored service at 10am this morning and are looking into the cause of 
the problem. If you had jobs queued/running at the time they will need 
to be resubmitted. We apologize for any inconvenience this may have caused.



From rhubley@systemsbiology.org Tue Apr  1 14:02:33 2008
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Subject: [Rmannounce] RepeatScout On Multiple Sequences
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RepeatScout is a highly successful de-novo repeat discovery algorithm 
developed by Price, A. L. et al. We have created a modified version of 
RepeatScout ( version 1.0.3 ) which supports searches on highly 
fragmented genomes. The new version does not attempt to extend seeds 
across sequence boundaries. Pavel Pevzner's lab has offered to host the 
download for this new version at: http://repeatscout.bioprojects.org/


From rhubley@systemsbiology.org Wed Apr 16 15:23:40 2008
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Subject: [Rmannounce] RepeatModeler Beta: Repeat Discovery Workbench Released
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RepeatModeler is a de-novo repeat family identification and modeling 
package. At the heart of RepeatModeler are two de-novo repeat finding 
programs ( RECON and RepeatScout ) which employ complementary 
computational methods for identifying repeat element boundaries and 
family relationships from sequence data. RepeatModeler assists in 
automating the runs of RECON and RepeatScout given a genomic database 
and uses the output to build, refine and classify consensus models of 
putative interspersed repeats.

The software is available for download at:  
http://www.repeatmasker.org/RepeatModeler.html

Also note that RepeatMasker is now up to version 3.2.1. This version as 
well as the previous version are organizational updates to support 
RepeatModeler and have little or no impact on RepeatMasker results.

From rhubley@systemsbiology.org Thu May  1 16:26:08 2008
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Subject: [Rmannounce] RepeatProteinMask Released,
	RepeatModeler/RepeatMasker Updates
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The program which runs the repeat protein search on the website is now 
available as a standalone program within the RepeatMasker package.

Thanks to the Sanger Institute and various testers we have patched a few 
bugs in the first RepeatModeler release.  The fixes required a new 
version of RepeatMasker to be created ( version 3.2.2 ) although the 
changes will not impact RepeatMasker results.  If you have experienced 
problems installing the first release or with running the repeat 
classifier, please download the latest RepeatMasker and RepeatModeler 
packages.



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The WUBlastXSearchEngine.pm module was missing from yesterday's 
RepeatMasker release. This module is needed for the RepeatProteinMask 
program. Please re-download the 3.2.2 release of RepeatMasker if you had 
previously obtained it.  Sorry for the inconvenience.

-R

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Subject: [Rmannounce] Pre-Masked Genomes Update - HG18 and MM9
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Today we updated the Pre-Masked Genomes page with the latest runs of 
RepeatMasker on the genome assemblies HG18 and MM9. In addition to the 
data query service we have also provided the ability to download the 
complete annotation sets as compressed files.

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  We have noticed a few times that RECON's "re-definition of elements ( 
eleredef )" appears to hang up ( in a recent run it sat on this step for 
over 6 hours before we killed it ).  If you also experience this problem 
while running RepeatModeler please let us know.  When we restart the run 
from the begining it has been able to accomplish this step in a 
reasonable amount of time ( hg18: 1-5 minutes ). 



From rhubley@systemsbiology.org Tue May 13 17:10:56 2008
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Subject: [Rmannounce] 
 Pre-Masked Genomes Update - Rice, Arabidopsis, Opossum, Platypus
 and Cow
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Today we updated the Pre-Masked Genomes page ( 
http://www.repeatmasker.org/cgi-bin/AnnotationRequest ) with the latest 
runs of RepeatMasker on the genome assemblies orySat5 (Rice), araTha5 
(Arabidopsis), monDom4 (Opossum), ornAna1 (Platypus), bosTau4 (Cow). The 
complete annotation sets are also available for these genomes as 
compressed files.

From rhubley@systemsbiology.org Wed May 21 10:36:18 2008
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Subject: [Rmannounce] RECON patched for 64bit processors
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We released a new version of RECON ( RECON1.06 ) which fixes problems 
users have experienced on 64bit platforms ( crashes, lockups ). For now 
you can download our version here: 
http://www.repeatmasker.org/RECON1.06.tar.gz. Please remember to update 
your RepeatModeler configuration ( by running "configure" ) if you 
install the new RECON in a different place than previous versions.

From rhubley@systemsbiology.org Tue Jun 10 14:33:39 2008
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Subject: [Rmannounce] DupMasker - A Tool for Annotating Primate Segmental
	Duplications
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In collaboration with Evan Eichler and Zhaoshi Jiang at the University 
of Washington we developed the DupMasker program. DupMasker uses a 
library of non-redundant consensus sequences of human segmental 
duplications, wherein a majority of the ancestral origins have been 
determined based on comparisons to mammalian outgroup genomes. Using 
DupMasker, new human and non-human primate (NHP) sequences may be 
readily queried to provide details on the origin and degree of sequence 
identity of each duplicon. This program can be applied to delineate the 
order and orientation of duplicons within complex duplication blocks and 
used to characterize structural variation differences between sequenced 
human haplotypes. The paper describing this work can be found in the 
latest issue of Genome Research
( http://www.genome.org/cgi/content/abstract/gr.078477.108v1?ck=nck ) 
and the software may be
downloaded from: http://www.repeatmasker.org/DupMaskerDownload.html

From rhubley@systemsbiology.org Wed Jun 11 11:13:14 2008
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Subject: [Rmannounce] Pre-Masked Genomes Update - Rhesus, Chicken, Rat, Cat,
	and Chimp
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The last few weeks we have updated the Pre-Masked Genomes page ( 
http://www.repeatmasker.org/cgi-bin/AnnotationRequest ) with the latest 
runs of RepeatMasker on the genome assemblies rheMac2 (Rhesus), galGal3 
(Chicken), rn4 (Rat), felCat3 (Cat), and panTro2 (Chimp). The complete 
annotation sets are also available for these genomes as compressed files.

From rhubley@systemsbiology.org Fri Jun 13 15:21:16 2008
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Subject: [Rmannounce] RepeatMasker, RepeatMasker Libraries,
	and RepeatScout Updates
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RepeatMasker open-3.2.5 was released ( 
http://www.repeatmasker.org/RMDownload.html ) along with an updated set 
of repeat libraries ( RM-20080611, RepBase 13.02 available from GIRI ). 
This release includes several fixes to the alignment output format ( 
single "X"s in the query portion of the alignment, incorrect sequence 
indexes in lines containing only gap characters "-" ) and an updated set 
of libraries for the RepeatProteinMask program. In addition a new 
release of RepeatScout is available for download ( 
http://repeatscout.bioprojects.org/ ). The RepeatScout 
filter-stage-1.prl script skipped the last sequence in the input file. 
Thanks to Gyorgy Abrusan for reporting this.

From rhubley@systemsbiology.org Thu Aug  7 14:51:07 2008
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Subject: [Rmannounce] RepeatMasker and RepeatMasker Libraries Updated
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RepeatMasker open-3.2.6 was released ( 
http://www.repeatmasker.org/RMDownload.html ) along with an updated set 
of repeat libraries ( RM-20080801,
including sequences up to RepBase 13.06 ). This release includes some 
repeat subclass nomenclature changes:

     Charlie     -> hAT-Charlie,      Fot1        -> TcMar-Fot1,
     MER1_type   -> hAT-Charlie,      MER2_type   -> TcMar-Tigger,
     MaLR        -> ERVL-MaLR,        Mariner     -> TcMar-Mariner,
     Pogo        -> TcMar-Pogo,       Tc1         -> TcMar-Tc1,
     Tc2         -> TcMar-Tc2,        Tc4         -> TcMar-Tc4,
     Tigger      -> TcMar-Tigger,     Tip100      -> hAT-Tip100, and
     hAT_Tol2    -> hAT-Tol2.

Also note that the *.tbl output file also reflect these changes.

From rhubley@systemsbiology.org Fri Aug  8 10:58:50 2008
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Subject: [Rmannounce] RepeatModeler/WUBlast and RepeatScout Bugs
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If you experience the error message: "Not found: ....." or "Identifiers 
not found: #" in RepeatModeler open-1.0.3 there is a simple fix. Edit 
the RepeatModeler script and change the line 1547 from:

  `$RepModelConfig::XDGET_PRGM -n $xdfDBFile -a$start -b$end "$seqID"`;

to:

  `$RepModelConfig::XDGET_PRGM -n -a$start -b$end $xdfDBFile "$seqID"`;

The error is caused by a parameter order dependency bug in WUBlast. We 
have also updated the RepeatScout release ( RepeatScout-1.0.5 ) with a 
bugfix to the filter-stage-1.prl script. Thanks to Eric Ganko and others 
for locating and reporting these problems.

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Subject: [Rmannounce] COSEG Beta Released
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COSEG is a program which automatically identifies repeat subfamilies 
using significant co-segregating ( 2-3 bp ) mutations.

This program is derived from three C programs and several perl scripts 
written by Alkes Price as part of an analysis of Alu elements in the 
human genome ( Whole-genome analysis of Alu repeat elements reveals 
complex evolutionary history, Alkes L. Price, Eleazar Eskin, and Pavel 
Pevzner, 2004 Genome Research ). The program was first adapted for use 
with other repeat families and then extended to support consideration of 
three co-segregating mutations using Alkes statistical model. In 2008 
with the help of Andy Siegel an alternative statistical model was 
developed and the codebase repackaged into the single source file.

The code may be downloaded from 
http://www.repeatmasker.org/COSEGDownload.html.

We appreciate user feedback on this new software package.

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Subject: [Rmannounce] 
	Pre-Masked Genomes Update - Drosophila, Mosquito, Fugu,
	and Zebrafish
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Today we updated the Pre-Masked Genomes page with the latest runs of 
RepeatMasker on the genome assemblies dm3 (Drosophila), anoGam1 
(Mosquito), fr2 (fugu), danRer5 (Zebrafish). The complete annotation 
sets are also available for these genomes as compressed files.

From rhubley@systemsbiology.org Thu Jan 29 16:16:41 2009
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Subject: [Rmannounce] New RepeatMasker and Libraries Released
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    RepeatMasker open-3.2.7 was released along with an updated set of 
repeat libraries ( RM-20090120, including most sequences up to RepBase 
13.11 ). This release includes a new approach to refining ALU 
annotations and coincides with the addition of several new ALU 
subfamilies to the databse. The database also includes the new 
Zebrafinch library.

-R

From rhubley@systemsbiology.org Thu Feb  5 10:56:10 2009
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Subject: [Rmannounce] Pre-Masked Genomes Update - Human, Zebrafinch,
 Zebrafish, Chicken, Frog, and Elephant
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Today we updated the Pre-Masked Genomes page with the latest runs of 
RepeatMasker ( 3.2.7 ) on the genome assemblies hg18 (Human), taeGut1 
(Zebrafinch), danRer5 (Zebrafish), galGal3 (Chicken), xenTro2 (Frog), 
and loxAfr2 (Elephant). The complete annotation sets are also available 
for these genomes as compressed files.

From rhubley@systemsbiology.org Tue Apr  7 16:01:08 2009
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We will be taking the RepeatMasker server down tomorrow ( Wednesday 
April 8th ) at 8:00 am PST for scheduled maintenance.  We expect no more 
than a half hour of downtime. 


-R

From rhubley@systemsbiology.org Thu Jun  4 13:16:31 2009
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Subject: [Rmannounce] New RepeatMasker and Libraries Released
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RepeatMasker open-3.2.8 was released along with an updated set of repeat 
libraries ( RM-20090604, including most sequences up to RepBase 14.04 ). 
The library has been submitted to GIRI and will be available shortly.

Notably this release includes support for the ABBlast search engine from 
Advanced Biocomputing. This is the commercial version of the academic 
program WUBlast ( which is no longer available ) and will hopefully be 
released sometime later this month to the general public. Also a major 
optimization bug was found in ProcessRepeats and fixed in this release. 
Minor bugfixes also included in this release include: fixes for 
Debian/Ubuntu use of the DASH shell, GFF format inconsistency, and some 
documentation fixes.

From rhubley@systemsbiology.org Tue Jul 14 17:30:49 2009
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Subject: [Rmannounce] Pre-Masked Genomes Update - Human, Mouse, Cow,
	Zebrafish, and Opossum
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Today we updated the Pre-Masked Genomes page ( 
http://www.repeatmasker.org/cgi-bin/AnnotationRequest ) with the latest 
runs of RepeatMasker ( RM-3.2.8 and db-20090604 ) on the genome 
assemblies hg19 (Human), bosTau4 (Cow), danRer6 (Zebrafish), and monDom5 
(Opossum). The complete annotation sets are also available for these 
genomes as compressed files by following a link from the above page.

From rhubley@systemsbiology.org Fri Oct 16 15:18:42 2009
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We have tested RepeatMasker with the newly released ABBlast ( comercial 
replacement for WUBlast ). If you have been having problems with 
obtaining WUBlast for use with RepeatModeler, or RepeatMasker please go 
to http://blast.advbiocomp.com/licensing/ for details on how to obtain 
this new version.

From rhubley@systemsbiology.org Thu May 13 10:42:30 2010
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Subject: [Rmannounce] RepeatMasker Cluster Upgrade
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On Tuesday May 11th we transitioned the RepeatMasker.org webservices 
over to a new cluster ( two of the three compute nodes are now online 
).  The new cluster should help us meet the demands on the server while 
leaving room for increased growth over the next few years.  We also 
upgraded the job scheduling software which should fix a few of the 
problems we experienced this past month.  Details on the new cluster can 
be found on the hardware page ( http://www.repeatmasker.org/server.html 
).  Sorry for any inconvenience the recent downtime has caused.

-Robert

From rhubley@systemsbiology.org Fri Jun 11 16:16:10 2010
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  We will have a brief period of server downtime on Saturday May, 12th at
  6:00am PST.  We only expect the system to be down for 15 minutes.  Please
  do not start jobs that won't complete before this time. We apologize for
  any inconvenience this causes.

-R

From rhubley@systemsbiology.org Thu Jul  1 14:01:41 2010
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 Today we released a new RepeatMasker ( open-3.2.9 ) on the website and 
for download. The new release adds two important updates:

        - RepeatMasker is now enabled to use RMBlast as a search engine. 
RMBlast is a modified version of NCBI's Blast suite which adds features 
needed for RepeatMasker's sensitive DNA searches. We are releasing 
pre-compiled versions for x64-linux and for Mac-intel as well as the 
source code.

        - Custom library searches are now possible without having to 
obtain the RepBase library. In the past the program required the user to 
install the RepBase repeat library even for searches using the "-lib 
mydatabase.fa" option. We do encourage the use of the RepBase library as 
RepeatMasker is optimised for use against this highly curated database.


From rhubley@systemsbiology.org Thu Jul  8 15:30:22 2010
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    Today we released a new RepeatModeler ( open-1.0.4 ) for download. 
The release adds support for the new RMBlast search engine and fixes a 
few small bugs in the previous release. To download the latest version 
please visit our download page at:
http://www.repeatmasker.org/RepeatModeler.html

-Robert 


From rhubley@systemsbiology.org Tue Aug  3 12:02:01 2010
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    Today we released a new version of COSEG ( 0.2.1 ). This release 
fixes a few bugs, switches the default statistical model and has 
improved code documentation. To download the latest version please visit 
our download page: http://www.repeatmasker.org/COSEGDownload.html

-Robert

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  Some users have been running into problems using the linux binary 
distribution of RMBLAST out of the box.  If you encounter an error such as:

NCBIBlastSearchEngine::setPathToEngine( /usr/local/rmblast/bin/rmblastn ): Cannot determine engine variant and version! at /usr/local/RepeatMasker/RepeatMasker line 576

It is very likely that the binary distribution is not compatible with 
your flavor of linux.  A quick test of this is to run rmblastn by hand 
to make sure it can be executed:

/usr/local/rmblast/bin/rmblastn -version

This should print out:

rmblastn: 2.2.23+
Package: rmblast[1.2] 2.2.23, build Jun 30 2010 14:13:01

If this operation fails you will probably need to compile your own 
version of rmblast for your platform.  Please download the source 
version and follow the instructions in the README file.

-Robert



From rhubley@systemsbiology.org Thu Oct  7 08:12:04 2010
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The RepeatMasker webservice ( www.repeatmasker.org ) was down due to a
problem with the recent automatic updates of Perl.  For some reason
CentOS/Redhat have broken the default settings for the Scalar::Util module
in their latest distributions.  We have fixed the problem and restored the
webservice for RepeatMasking jobs.  Sorry for any inconvenience this may
have caused.  If you run RepeatMasker locally you may be experiencing the
same problem and will need to update or reinstall your Scalar::Util perl
module.  The error message from RepeatMasker/Perl looks like this:

weaken is only available with the XS version of Scalar::Util at
/u1/local/rmserver/share/ArrayList.pm line 69
BEGIN failed--compilation aborted at /u1/local/rmserver/share/ArrayList.pm
line 69.
Compilation failed in require at
/u1/local/rmserver/share/SearchResultCollection.pm line 74.
Compilation failed in require at /usr/local/rmserver/share/RepeatMasker line
340.
BEGIN failed--compilation aborted at /usr/local/rmserver/share/RepeatMasker
line 340.

Please let me know if you have any questions this.

-Robert

--00504502f681ed71b00492085078
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The RepeatMasker webservice ( www.r=
epeatmasker.org ) was down due to a problem with the recent automatic u=
pdates of Perl.=A0 For some reason CentOS/Redhat have broken the default se=
ttings for the Scalar::Util module in their latest distributions.=A0 We hav=
e fixed the problem and restored the webservice for RepeatMasking jobs.=A0 =
Sorry for any inconvenience this may have caused.=A0 If you run RepeatMaske=
r locally you may be experiencing the same problem and will need to update =
or reinstall your Scalar::Util perl module.=A0 The error message from Repea=
tMasker/Perl looks like this:


weaken is only available with the XS version of =
Scalar::Util at /u1/local/rmserver/share/ArrayList.pm line 69
BEGIN fail=
ed--compilation aborted at /u1/local/rmserver/share/ArrayList.pm line 69.

Compilation failed in require at /u1/local/rmserver/share/SearchResultColle=
ction.pm line 74.
Compilation failed in require at /usr/local/rmserver/s=
hare/RepeatMasker line 340.
BEGIN failed--compilation aborted at /usr/lo=
cal/rmserver/share/RepeatMasker line 340.


Please let me know if you have any questions this.

-Robert


--00504502f681ed71b00492085078--

From rhubley@systemsbiology.org Tue Dec 28 10:37:11 2010
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Subject: [Rmannounce] RepeatMasker cluster downtime
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   The RepeatMasker cluster will be down on Wednesday, December 29th at 
10am PST
for approximately 10 minutes.  Please be sure to schedule your jobs to 
complete
by that time.


From rhubley@systemsbiology.org Thu Apr  7 09:04:11 2011
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**//The Institute for Systems Biology is moving locations this weekend. 
Unfortunately this means that the servers which run RepeatMasker will be 
offline during this time. They are projecting downtime from tomorrow ( 
Friday April 8th ) to Tuesday ( April 12th ). We apologize for the 
inconvenience and the late notice.

--------------070809020903060004020506
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     The Institute for Systems Biology
    is moving locations this weekend. Unfortunately this means that the
    servers which run RepeatMasker will be offline during this time.
    They are projecting downtime from tomorrow ( Friday April 8th ) to
    Tuesday ( April 12th ). We apologize for the inconvenience and the
    late notice.
  


--------------070809020903060004020506--

From rhubley@systemsbiology.org Tue Apr 26 16:29:22 2011
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/Tuesday April 26, 2011/

    Today we released a new RepeatMasker ( open-3.3.0 ) along with an
    updated set of repeat libraries ( RM-20110914, including most
    sequences up to RepBase 16.01 ). The new release includes the
    following changes:

        * Compatable with the lastest versions of RMBlast
        * Updated reporting of databases used in the search
        * New taxonomy database imported from NCBI
        * Fixed error "refinelib doesn't exist" when -species option is used
        * Perl 5.12.2 and later deprecated the use of "defined" for hash
          variables

    The new release is available here:
    http://www.repeatmasker.org/RMDownload.html 


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     Tuesday
          April 26, 2011 
    
 Today we released a new RepeatMasker ( open-3.3.0 )
      along with an updated set of repeat libraries ( RM-20110914,
      including most sequences up to RepBase 16.01 ). The new release
      includes the following changes:
      
    
        
  • Compatable with the lastest versions of RMBlast
    • 
        
  • Updated reporting of databases used in the search
    • 
        
  • New taxonomy database imported from NCBI
    • 
        
  • Fixed error "refinelib doesn't exist" when -species option
          is used
    • 
        
  • Perl 5.12.2 and later deprecated the use of "defined" for
          hash variables
    • 
      

      The new release is available here: http://www.repeatmasker.org/RMDownload.html
    

  


--------------080002060003070009030504--

From rhubley@systemsbiology.org Mon Jun  6 15:14:07 2011
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Subject: [Rmannounce] New RepeatModeler Released ( 1.0.5 ) - Bugfix
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Today we released a new RepeatModeler ( open-1.0.5 ) to fix a critical 
bug with runs using the RMBlast search engine. The results produced by 
RMBlast were being mis-interpreted by the model refinement algorithm. 
The resulting consensi were produced with mis-aligned input data. NOTE: 
This problem only impacts runs using RMBlast. ABBlast and previous 
WUBlast runs would not have been affected. The new release is available 
here: http://www.repeatmasker.org/RepeatModeler.html

From rhubley@systemsbiology.org Wed Jun  8 14:42:48 2011
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We have a patch for recent versions of RepeatMasker 3.2.X and higher 
which allows the program to work with the most-recent version of 
Crossmatch ( 1.080812 ). Without this patch the program will 
intermittently report "FastaDB::substr - Error index out of bounds! at 
RepeatMasker line 4969" when used with this version of Crossmatch. The 
patch is easy to apply. Simply replace the CrossmatchSearchEngine.pm 
module in your RepeatMasker directory with this one: 
http://www.repeatmasker.org/CrossmatchSearchEngine.pm 



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    We have
    a patch for recent versions of RepeatMasker 3.2.X and higher which
    allows the program to work with the most-recent version of
    Crossmatch ( 1.080812 ). Without this patch the program will
    intermittently report "FastaDB::substr - Error index out of bounds!
    at RepeatMasker line 4969" when used with this version of
    Crossmatch. The patch is easy to apply. Simply replace the
    CrossmatchSearchEngine.pm module in your RepeatMasker directory with
    this one: http://www.repeatmasker.org/CrossmatchSearchEngine.pm
    

    

  


--------------070109060508060906060208--

From rhubley@systemsbiology.org Thu Jun  9 10:35:06 2011
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**//We released a new version of RECON ( RECON1.07 ) which workarounds a 
rare problem with division by zero in the original RECON code. The 
workaround is a temporary measure to avert the division by zero but 
doesn't fix the underlying problem which is as yet undiagnosed. A 
warning is produced when the workaround is invoked. Using this version 
allows for long RepeatModeler runs to complete despite one rare case 
exercising this bug. For now you can download our version here: 
http://www.repeatmasker.org/RECON-1.07.tar.gz. Please remember to update 
your RepeatModeler configuration ( by running "configure" ) if you 
install the new RECON in a different place than previous versions.

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     We released a new version of
    RECON ( RECON1.07 ) which workarounds a rare problem with division
    by zero in the original RECON code. The workaround is a temporary
    measure to avert the division by zero but doesn't fix the underlying
    problem which is as yet undiagnosed. A warning is produced when the
    workaround is invoked. Using this version allows for long
    RepeatModeler runs to complete despite one rare case exercising this
    bug. For now you can download our version here: http://www.repeatmasker.org/RECON-1.07.tar.gz.
    Please remember to update your RepeatModeler configuration ( by
    running "configure" ) if you install the new RECON in a different
    place than previous versions.
  


--------------000308030706070607010108--

From rhubley@systemsbiology.org Wed Sep 21 11:54:24 2011
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Date: Wed, 21 Sep 2011 11:52:13 -0700
From: Robert Hubley 
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Subject: [Rmannounce] New RepeatMasker Libraries
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Today we updated the RepeatMasker libraries to version rm-20110920. This 
update includes new RepBase sequences up to RepBase 16.08, 30+ new 
ancient mammalian elements derived from the Laurasiatherian 
reconstruction, as well as numerous classification improvements.  The 
new database may be downloaded from GIRI: http://www.girinst.org/


From rhubley@systemsbiology.org Tue Feb 14 10:58:39 2012
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Date: Tue, 14 Feb 2012 10:57:31 -0800
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Subject: [Rmannounce] Pre-Masked Genomes Update - Human, Rat, Bat, Pig,
 Rabbit, Sea urchin, Lancelet, Guinea pig, Stickleback, and Ciona
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Today we updated the Pre-Masked Genomes Search 
 page and the 
Pre-Masked Genomes Download 
 page with the latest 
runs of RepeatMasker ( RM-3.3.0 and db-20120124 ) on the genome 
assemblies hg19 (Human), rn4 (Rat), myoLuc2 (Bat), susScr2 (Pig), 
oryCun2 (Rabbit), strPur2 (Sea urchin), braFlo1 (Lancelet), cavPor3 
(Guinea pig), gasAcu1 (Stickleback), and ci2 (Ciona tunicate).

Cheers,

-Robert

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    Today we updated the Pre-Masked
      Genomes Search page and the Pre-Masked
      Genomes Download page with the latest runs of RepeatMasker (
    RM-3.3.0 and db-20120124 ) on the genome assemblies hg19 (Human),
    rn4 (Rat), myoLuc2 (Bat), susScr2 (Pig), oryCun2 (Rabbit), strPur2
    (Sea urchin), braFlo1 (Lancelet), cavPor3 (Guinea pig), gasAcu1
    (Stickleback), and ci2 (Ciona tunicate).

    

    Cheers,

    

    -Robert

  


--------------030605040709020307010301--

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Date: Thu, 22 Mar 2012 15:13:41 -0700
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Subject: [Rmannounce] Pre-Masked Genomes Update - Tree Shrew, Armadillo,
 Sloth, Hyrax, Hedgehog, Alligator, and Lizard
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Today we updated the RepeatMasker full genome datasets page adding some 
new genomes run with RepeatMasker ( RM-3.3.0 and db-20120124 ). The new 
assemblies include: tupBel1 (Tree Shrew), dasNov2 (Armadillo), choHof1 
(Sloth), proCap1 (Hyrax), eriEur1 (Hedgehog), allMis (Alligator), and 
anoCar2 (Lizard).

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    Today we updated the RepeatMasker full genome datasets page adding
    some new genomes run with RepeatMasker ( RM-3.3.0 and db-20120124 ).
    The new assemblies include: tupBel1 (Tree Shrew), dasNov2
    (Armadillo), choHof1 (Sloth), proCap1 (Hyrax), eriEur1 (Hedgehog),
    allMis (Alligator), and anoCar2 (Lizard).
  


--------------090108080108080900040302--

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Date: Thu, 22 Mar 2012 15:14:29 -0700
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Subject: [Rmannounce] Repeat Landscapes And New Download Pages
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We have expanded upon the "Pre-Masked Genomes Download" page at the 
repeatmasker website. We have made it easier to navigate to the species 
of interest using a tree view of our datasets. In addition to the 
ability to download annotation and alignment files for various 
assemblies/libraries, you will also find repeat landscapes for the 
latest RepeatMasker runs. Repeat landscapes depict the relative 
abundance of repeat classes in the genome versus the Kimura divergence 
from the consensus. The landscapes are a useful tool for visualizing the 
activity of transposable elements over time. The new page is listed as 
Genomic Analsysis and Downloads 
 
under the Service menu at the top left of the main site.

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    We have expanded upon the "Pre-Masked Genomes Download" page at the
    repeatmasker website. We have made it easier to navigate to the
    species of interest using a tree view of our datasets. In addition
    to the ability to download annotation and alignment files for
    various assemblies/libraries, you will also find repeat landscapes
    for the latest RepeatMasker runs. Repeat landscapes depict the
    relative abundance of repeat classes in the genome versus the Kimura
    divergence from the consensus. The landscapes are a useful tool for
    visualizing the activity of transposable elements over time. The new
    page is listed as Genomic
      Analsysis and Downloads under the Service menu at the top left
    of the main site.
  


--------------010106040906070508010500--

From rhubley@systemsbiology.org Thu Apr 19 15:33:16 2012
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Date: Thu, 19 Apr 2012 15:32:38 -0700
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Subject: [Rmannounce] New RepeatMasker Libraries
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Today we updated the RepeatMasker libraries to version rm-20120418. This 
update includes new RepBase sequences up to RepBase 17.02, including 
significant additions for lizard, potato and soybean.  We have also 
extended many ancient elements with the aid of the crocodile genome and 
Laurastherian reconstruction.  The new database may be downloaded from 
GIRI: http://www.girinst.org

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Date: Fri, 22 Jun 2012 11:21:34 -0700
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Subject: [Rmannounce] RepeatMasker open-3-3-0 Crossmatch Patch
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RepeatMasker + Crossmatch users have reported an intermittent bug with 
RepeatMasker open-3-3-0. On runs using Crossmatch as the search engine 
the following error can appear:

         WARNING: The search engine returned an error (141)
         A search phase could not complete on this batch.
         The batch file will be re-run and if possible the
         program will resume.
         WARNING: Retrying batch ( 1 )...

In some cases this is caused by a bug in the file 
"CrossmatchSearchEngine.pm". To fix this problem either download the 
patched version of the RepeatMasker-open-3-3-0 package from 
http://www.repeatmasker.org/RMDownload.html  or you can simply download 
the new CrossmatchSearchEngine.pm 
 
file and replace the old one with it. Please submit feedback 
 
if you have any problems with this process.


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    RepeatMasker + Crossmatch users have reported an intermittent bug
    with RepeatMasker open-3-3-0. On runs using Crossmatch as the search
    engine the following error can appear:
    

    

    
        WARNING: The search engine returned an error (141)
        A search phase could not complete on this batch.
        The batch file will be re-run and if possible the
        program will resume.
        WARNING: Retrying batch ( 1 )...


    

      In some cases this is caused by a bug in the file
      "CrossmatchSearchEngine.pm". To fix this problem either download
      the patched version of the RepeatMasker-open-3-3-0 package from
      http://www.repeatmasker.org/RMDownload.html  or you can simply
      download the new CrossmatchSearchEngine.pm
      file and replace the old one with it. Please submit feedback
      if you have any problems with this process.
    

  


--------------090305090300090703050007--

From rhubley@systemsbiology.org Tue Jun 26 14:58:43 2012
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Date: Tue, 26 Jun 2012 14:58:04 -0700
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Subject: [Rmannounce] Analysis of Human ALU Subfamilies
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As often happens in science, an analysis is performed to improve the 
overall performance of a program ( RepeatMasker ) and once a new version 
of the program is out we forget about the datasets themselves. Today we 
uploaded the results of a coseg run on over 500k human ALUs. Follow this 
link ( 
http://www.repeatmasker.org/AluSubfamilies/humanAluSubfamilies.html ) to 
see the tree produced by coseg along with a multiple alignment of the 
various subfamilies, old and new ( at the time ).

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    As often happens in science, an analysis is performed to improve the
    overall performance of a program ( RepeatMasker ) and once a new
    version of the program is out we forget about the datasets
    themselves. Today we uploaded the results of a coseg run on over
    500k human ALUs. Follow this link (
    http://www.repeatmasker.org/AluSubfamilies/humanAluSubfamilies.html
    ) to see the tree produced by coseg along with a multiple alignment
    of the various subfamilies, old and new ( at the time ).
    
  


--------------010208000409060908010702--

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Date: Thu, 13 Sep 2012 14:21:58 -0700
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Subject: [Rmannounce] Dfam: A Database for Profile HMMs of Transposable
	Elements
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The first version of a transposable element profile HMM database was 
released this month. This represents a major improvement in the 
characterization of these interesting sequences. Profile methods are 
known to improve sensitivity over single sequence search, with profile 
HMMs in particular leveraging the additional information content in 
position-specific residue and indel variability. Until very recently the 
use of DNA/DNA profile HMMs to conduct large scale genomic searches was 
impractical. Advances by the HMMER3 development team at HHMI Janelia 
farm have made genome scale searches of profile HMMs feasible and 
enabled the development of this new community resource. A new version of 
RepeatMasker which uses Dfam and nhmmer will be released in the next few 
weeks. This work is a collaboration between HHMI Janelia Farm, GIRI ( 
Genetic Information Research Institute, Repbase ), and the Institute for 
Systems Biology.

The official announcement of the resource: 
http://selab.janelia.org/people/eddys/blog/?p=675

The database website: http://dfam.janelia.org

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    The first version of a transposable element profile HMM database was
    released this month. This represents a major improvement in the
    characterization of these interesting sequences. Profile methods are
    known to improve sensitivity over single sequence search, with
    profile HMMs in particular leveraging the additional information
    content in position-specific residue and indel variability. Until
    very recently the use of DNA/DNA profile HMMs to conduct large scale
    genomic searches was impractical. Advances by the HMMER3 development
    team at HHMI Janelia farm have made genome scale searches of profile
    HMMs feasible and enabled the development of this new community
    resource. A new version of RepeatMasker which uses Dfam and nhmmer
    will be released in the next few weeks. This work is a collaboration
    between HHMI Janelia Farm, GIRI ( Genetic Information Research
    Institute, Repbase ), and the Institute for Systems Biology.

    

    The official announcement of the resource:
    http://selab.janelia.org/people/eddys/blog/?p=675

    

    The database website: http://dfam.janelia.org
  


--------------070502040300050802040203--

From rhubley@systemsbiology.org Fri Sep 14 16:19:17 2012
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Subject: [Rmannounce] NCBI Releases BLAST+/RMBlast 2.2.27
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In collaboration with NCBI we now have a synchronized release of the 
RMBlast and NCBI BLAST+ tools. NCBI now hosts the source code and 
pre-compiled binaries for RMBlast allowing us to support a more diverse 
set of hardware/software platforms. Please see our RMBlast page ( 
http://www.repeatmasker.org/RMBlast.html ) for details on how to install 
the new release with RepeatMasker and RepeatModeler. Special thanks to 
George Coulouris at NCBI for all his assistance in getting this 
distribution system setup.



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Subject: [Rmannounce] RepeatMasker 4.0
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Today we released RepeatMasker 4.0 adding support for the new nhmmer 
program and the new profile HMM database of transposable elements - 
Dfam. Other changes include: a new alignment file format for improved 
cross referencing of database/annotation identifiers, adoption of TRF 
for simple repeat identification, improved SINE subfamily refinement, 
and plenty of bugfixes. The new release is available 
here:http://www.repeatmasker.org/RMDownload.html. 


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    Today we released RepeatMasker 4.0 adding support
      for the new nhmmer program and the new profile HMM database of
      transposable elements - Dfam. Other changes include: a new
      alignment file format for improved cross referencing of
      database/annotation identifiers, adoption of TRF for simple repeat
      identification, improved SINE subfamily refinement, and plenty of
      bugfixes. The new release is available here: http://www.repeatmasker.org/RMDownload.html.
  


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Subject: [Rmannounce] RepeatMasker 4.0.1 Maintenance Release
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Today we released RepeatMasker 4.0.1. This is a maintenance update which 
fixes problems observed by some of our users. Notably this fixes error 
messages produced by the configure script, problems using the older 
wublast program with RepeatMasker, empty classname columns when custom 
libraries are used, and noisy perl warnings. Also included in this 
release are an updated taxonomy database, and an expanded repeat protein 
database. The new release is available 
here:http://www.repeatmasker.org/RMDownload.html

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    Today we released RepeatMasker 4.0.1. This is a
      maintenance update which fixes problems observed by some of our
      users. Notably this fixes error messages produced by the configure
      script, problems using the older wublast program with
      RepeatMasker, empty classname columns when custom libraries are
      used, and noisy perl warnings. Also included in this release are
      an updated taxonomy database, and an expanded repeat protein
      database. The new release is available here: http://www.repeatmasker.org/RMDownload.html
  


--------------020909010205000004070601--

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Date: Mon, 29 Apr 2013 13:38:02 -0700
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Subject: [Rmannounce] RepeatMasker 4.0.2 Maintenance Update and New Library
	Release
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Today we released RepeatMasker 4.0.2. This is a maintenance update which 
fixes several problems in 4.0.0/4.0.1. Notably there were issues with 
human Alu refinement, short input sequences producing "FastaDB::substr - 
Error index out of bounds!" errors, and lastly an issue with overlapping 
annotations not being merged. We have also released a new RepeatMasker 
library ( rm-20130422 ) which includes updates from Repbase as well as 
four new genome libraries: Gibbon (Nomascus leucogenys), American 
alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus 
porosus), and gharial (Gavialis gangeticus). The new release is 
available here: http://www.repeatmasker.org/RMDownload.html. 


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    Today we released
      RepeatMasker 4.0.2. This is a maintenance update which fixes
      several problems in 4.0.0/4.0.1. Notably there were issues with
      human Alu refinement, short input sequences producing
      "FastaDB::substr - Error index out of bounds!" errors, and lastly
      an issue with overlapping annotations not being merged. We have
      also released a new RepeatMasker library ( rm-20130422 ) which
      includes updates from Repbase as well as four new genome
      libraries: Gibbon (Nomascus leucogenys), American alligator
      (Alligator mississippiensis), saltwater crocodile (Crocodylus
      porosus), and gharial (Gavialis gangeticus). The new release is
      available here: http://www.repeatmasker.org/RMDownload.html.
  


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