I'm reading a paper about genome assembly and analysis.
and it says "Swiss-Prot comparisons were done using protein BLAST alignments with BLAST+ (v2.3.0), e-value cut-off 1 × 10−5, -max_target_seqs 100, -max_hsps 1, and locally optimal Smith-Waterman alignments (-use_sw_tback)".
what is Smith-Waterman? and Smith-Waterman alignment?
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written
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jth6974 •
1 answer
Swiss-Prot is a manually curated database of proteins, available here: https://www.uniprot.org
Smith-Waterman is one of the more basic bioinformatics alignments for local sequence alignments, which is an optional setting in BLAST. Smith-Waterman is much more slower than BLAST's standard algorithm, while it's more precise (look here for a larger comparison by the CLC people)
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