Bioperl: software announcement

Ian Korf
Tue, 30 May 2000 11:38:32 -0500 (CDT)


Some software that may be of interest.

Licensing issues have been resolved (at least for academics). MaskerAid
makes RepeatMasker run ~35 times faster. There's a mailto link at the
website ( to get the software. I'm
not sure what's up with commercial licenses.

Makes BLASTN run much faster by multiplexing small queries. The speed-up
depends on a lot of factors, but is around 10x with read-sized querries.
Still under development, so feedback is appreciated. Works with both
WU-BLAST and NCBI-BLAST. Free too (

Question: Is anyone working with Prosite? I just made a script that
finds all ORFs (minimum size cutoff) with Prosite patterns (probability
cutoff) in genomic DNA. Useful to anyone? Something similar out there?
Someone interested in viral genes asked for it, but it may be of general

-Ian Korf
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