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Posts by martinsteinegger
... I am biased since I am the developers of [MMseqs2]. MMseqs2 can perform fast sequence/profile searches. It is possible to annotate 1.1 billion protein sequences with Pfam domains in 8.3 h on a 2×14-core server. [Here] is a guide how to setup the search. : https://github.com/soedinglab/M ...
... We compute the reverse complement k-mer in [MMseqs2] using SIMD. The trick is to use two lookup tables (lookup1 and lookup2) for the reverse complements. The function should be roughly 1.3x times as fast as revcomp64_v2. It can probably still be optimized more. // Compute reverse complement ...
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