Question: what is Swiss-Prot comparison?
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gravatar for jth6974
11 weeks ago by
jth697410
jth697410 wrote:

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?

swiss-prot comparison • 169 views
ADD COMMENTlink modified 11 weeks ago by Philipp Bayer6.0k • written 11 weeks ago by jth697410
3
gravatar for Philipp Bayer
11 weeks ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

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)

ADD COMMENTlink written 11 weeks ago by Philipp Bayer6.0k
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