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Help me with BLAST pairwise alignment parameters
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15 months 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

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

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

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