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Fastest Protein Sequence Similarity Search Algorithm

I heard of RapSearch2 which claims to be must faster than blast and HMMER which is as fast as Blast. I am wondering if there is any benchmark of such programs since the RefSeq/TrEMBL sequence database is growing too fast. Thanks

blast
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updated by cdsouthan cdsouthan • written by Pappu Pappu

Rapsearch2 works really fast for me, but also takes quite some memory. In the first Rapsearch paper is a runtime comparison to blast.

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written by pmenzel • pmenzel

1 answer

Try UniRef90, ~ half the size.

As comment, it would be useful if NCBI could make an nr 90 as well, or maybe EBI a UniRef 70 (i.e. between 90 and 50)

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written by cdsouthan cdsouthan

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