User: martinsteinegger

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Posts by martinsteinegger

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Answer: A: high-throughput domain discovery
... I am biased since I am the developers of [MMseqs2][1]. 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][2] is a guide how to setup the search. [1]: https://github.com/soedinglab/M ...
written 3 months ago by martinsteinegger20
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Answer: A: Fast kmer reverse complement code using bit tricks
... We compute the reverse complement k-mer in [MMseqs2][1] 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 ...
written 5 months ago by martinsteinegger20

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