This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How can I run multiple sequence alignment for a large number of proteins (~10k)

What's the preferred method for running multiple sequence alignment on such a large amount of protein sequences? I'm trying something fairly experimental and running MSA would be really helpful in the approach.

I usually use muscle and noticed there is a super5 module that helps with this: https://drive5.com/muscle5/manual/cmd_super5.html

How can I adjust the parameters to help out with running out of memory? Alternatively, is there another tool that's better suited for this? Basically, I want a fasta MSA for the output.

muscle msa protein multiple alignment sequence
• 2,851 views • link
updated by Mensur Dlakic Mensur Dlakic • written by O.rka O.rka

I should have mentioned that some of the sequences are long. There are a few that are ~70k. I've trimmed them out and it's working now but I'll keep MAFFT in the back of my in case this fails.

• 0 views • link
written by O.rka O.rka

1 answer

As advertised in their paper, FAMSA is meant specifically for aligning huge protein families. Clustal Omega should work as well.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Wow, FAMSA is really fast AND memory efficient. Nice find thank you! Do you usually use single linkage, upgma, or nj?

• 0 views • link
written by O.rka O.rka

I have always used single linkage but with proteins that were not as long as yours. If speed and memory are not problematic for your computer setup, that should be the best choice.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Log in to answer this question.

More posts like this