Question: Help me with BLAST pairwise alignment parameters
0
gravatar for Alec Watanabe
3 months ago by
Alec Watanabe30 wrote:

Hi, if I were to run BLAST pairwise alignments to find sequence similarities as the initial step for protein clustering, just like other softwares employ for pan genomic analyses, would a 75% coverage provide me with significant matches given that I'm working with genomes with 92%+ similarity? Is this coverage value too stringent, ok or too loose in this case and why? Thank you

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 3 months ago by Alec Watanabe30
1

This is quite relative scenario, changing from case to case. You havent mentioned anything about e-value. Go through this paper once

ADD REPLYlink written 3 months ago by bioExplorer3.7k

Thank you, I will give it a read today. By the way, E-value should be 1e-05.

ADD REPLYlink written 3 months ago by Alec Watanabe30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1316 users visited in the last hour