Is there a faster alternative to ncbi blast for searching for distantly related homologs in huge databases such as nr?
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You might look at USEARCH/UBLAST (http://drive5.com/usearch/). I'm not sure how the latest versions of USEARCH compare to the latest versions of blast+. I'm guessing it will depend on the degree of divergence you want to allow in your searches. The author of USearch talked about some of the tradeoffs regarding speed and sensitivity here (three years ago) http://www.biostars.org/p/1241/ .
I'd be interested to see what other people think about this too. -
HMMER is very fast in my experience (although their site states that it's essentially as fast as blast)..savetherhino.orgComment
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RAPsearch2 is 50-100X faster than blastx and Pauda claims to be even faster than thatComment
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