This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Removing redundant sequences

I have a fasta file containing many protein sequences with identifier. How can I remove the redundant sequences using HMMscan

sequence alignment blast
• 6,296 views • link
updated by Ram Ram • written by kutubjoy • kutubjoy

Why use HMMscan to remove redundant sequences? There are a gazillion deduplication tools out there - just search the forum for FASTA deduplication.

• 0 views • link
written by Ram Ram

Hello guys

I have more than 70,000 protein sequences come from 65 animal species, most of them are TFs. So some of them might be homologous. I like to use CD-HIT to remove the them. But which similarity threshold should I use?

Any suggestion?

• 0 views • link
updated by Ram Ram • written by Kurban Kurban

I see that you've created a Tool type post for your tool. Please do not spam threads with ads for your tool.

• 0 views • link
written by Ram Ram

2 answers

I wrote a perl script to do that. It is called remove_duplicates and you can find it here:

https://github.com/nterhoeven/sequence_processing

• 0 views • link
written by nterhoeven nterhoeven

As Ram suggested, there are several tools to do this, one is cd-hit.

• 0 views • link
updated by Ram Ram • written by h.mon h.mon

This is an old question :)

• 0 views • link
written by Ram Ram

Not for my standards, I even replied to 3-4 year old questions ;-)

• 0 views • link
updated by Ram Ram • written by h.mon h.mon

Log in to answer this question.

More posts like this