Bioinformatics Advance Access published online on November 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti774
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1 National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bldg. 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894 USA
* To whom correspondence should be addressed.
Motivation: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase library, that may not exist for newly sequenced genomes. Results: We have developed a software tool called WindowMasker (WM) that identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. WM is orders of magnitude faster than RM because WM uses a few linear-time scans of the genome sequence, rather than local alignment methods that compare each library sequence to each piece of the genome. We validate WM by comparing BLAST outputs from large sets of queries applied to two versions of the same genome, one masked by WM, and the other masked by RM. Even for genomes such as the human genome, where a good RepBase library is available, searching the database as masked with WM yields more matches that are apparently nonrepetitive and fewer matches to repetitive sequences. We show that these results hold for transcribed regions as well. WM also performs well on genomes for which much of the sequence was in draft form at the time of the analysis. Availability: WM is included in the NCBI C++ toolkit. The source code for the entire toolkit is available at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/.
Received July 26, 2005
Revised November 8, 2005
Accepted November 8, 2005
Article
WindowMasker: window based masker for sequenced genomes
Aleksandr Morgulis 1 *,
E. Michael Gertz 1,
Alejandro A. Schäffer 1,
and
Richa Agarwala 1 *
Richa Agarwala, E-mail: richa{at}helix.nih.gov
Abstract
* under contract to MSD Inc., Fairfax, VA, USA
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