what is Swiss-Prot comparison?

Question

[jth6974]

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?

Answer 1

[Philipp Bayer]

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)