A new version of the RepeatMasker repeat library ( RMLib: 20071204, RepBase: 12. 06 ) is now available for download from GIRI.

We replaced the main RepeatMasker webserver today with a new dual Xeon quad core server with 8GB of main memory. The new server also contains increased disk storage for expansion of the cached genomes.

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.

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-2.tar.gz. NOTE: You may have to alter the first line in ProcessRepeats to correctly reference your perl installation location.

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.

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:
  • 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!".
  • Division By Zero Bugfix: Under special circumstances ProcessRepeats produces a "Illegal division by zero at ProcessRepeats line 1860." error.
  • Long Sequence Names Bugfix: Long sequence names > 20 characters can cause ProcessRepeats to fail. Thanks to Gordon Lack for finding and reporting this.
  • Negative Sequence Positions Bugfix: ProcessRepeats was reporting negative sequence positions in the final output file.

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.

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.