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Bioinformatics Vol. 16 no. 11 2000
Pages 1040-1041
© 2000 Oxford University Press

Applications Note

MaskerAid : a performance enhancement to RepeatMasker

Joseph A. Bedell 1,**, Ian Korf 1, and Warren Gish 1,*

1 Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA

Received on May 22, 2000 ; revised on July 18, 2000 ; accepted on July 21, 2000

Summary: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid , a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting.

Availability: On request from the authors (see http://sapiens.wustl.edu/MaskerAid).

Contact: maskeraid{at}watson.wustl.edu

These authors contributed equally to this work.

* To whom correspondence should be addressed.

** Current address: Incyte Genomics, 4633 World Parkway Cir., St. Louis, MO 63134 USA, jbedell@incyte.com


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