[Bioperl-l] short motif searches

Jyoti Shah jyotikshah at gmail.com
Mon Oct 23 07:10:43 UTC 2006


I am interested in searching motifs as small as 6 or 7 nucleotides in
genomic databases. I need exact matches. Is there any bioperl module
available which can help me do this? I tried WU BLAST with word size one,
but I am getting warning messages such as "WARNING: the maximum achievable
score of 7 in context 0 (frame +1) is less than the ungapped cutoff score S2
(=13). Exit code 0...". Any suggestions?

Thanks in advance,

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