Fastest Protein Sequence Similarity Search Algorithm

Question

[Pappu]

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

[pmenzel]

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

Answer 1

[cdsouthan]

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)