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@watson.wustl.edu