This is a test version of Biostars. For the public version, visit https://www.biostars.org.
can we retrieve protein sequences from the clusters of CD-hit?

Hello Can we retrieve all protein sequences in fasta forrmat from the clusters we get from CD-Hit?

cd-hit protein sequences
• 3,848 views • link
updated by Md • Md • written by sharmatina189059 • sharmatina189059

There is not enough information in this one line question to provide a useful answer. Please add additional details. What are you clustering (DNA/Protein)? Where do you want to retrieve the sequence from?

• 0 views • link
written by GenoMax GenoMax

I am running this command :

cd-hit -i merge_all_788_proteins.faa -o out_788_cd-hit50 -c 0.5 -n 2 -M 0

This gives me a fasta file having all the representative sequences (longest one) and .clust file having all the clusters file.

I need to get all protein sequences from clusters0 or cluster 1 and so on for their multiple sequence alignment.

• 0 views • link
updated by Ram Ram • written by sharmatina189059 • sharmatina189059

make_multi_seq.pl (LINK) included in CD-HIT will do what you need based on the description.

• 0 views • link
written by GenoMax GenoMax

For doing CD-HIT cluster do we have to merge all proteine in single file, if so how we will do it, or is it possible to do clustering all fasta file by keeping in single directory,

• 0 views • link
written by Md • Md

1 answer

I have code that will work to achieve this:

https://github.com/jrjhealey/bioinfo-tools/blob/master/ParseCDHIT.py

Just be aware that because of a limitation of the way CD-HIT writes the names out, all your sequences must be uniquely named (and ideally short). You will also need to ensure you run CD-HIT with the -d parameter set to 0.

• 0 views • link
written by Joe Joe

Log in to answer this question.

More posts like this