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

Join Date: Aug 2009
Posts: 245
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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.
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Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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