Help me with BLAST pairwise alignment parameters
0
0
Entering edit mode
5.9 years ago

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

BLAST pairwise alignment parameters • 1.4k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1785 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6