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Old 02-12-2015, 11:04 AM   #15
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Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

Depending on what you are looking for and your stringency requirements, could you switch to BLAT instead? Maybe adopt a tiered approach of a first pass with BLAT to reduce the search space, then BLAST or HMMER (in parallel runs) for the higher stringency search on selected hits.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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