This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting Names Of Proteins Around A Protein In A Genome

I have a list of uniprot IDs of a protein in different species. Now I want to list the names of proteins around it (2 upstream and 2 downstream) in various genomes. Let me know if there is any tool for that. Thanks.

python
• 2,397 views • link
updated by Raygozak Raygozak • written by Pappu Pappu

You mean "the names of proteins encoded by the genes around it." Upstream/downstream refers to genes, not proteins.

Also - what have you tried or searched for? There's no evidence that you've tried to address this problem yourself.

• 0 views • link
written by Neilfws Neilfws

1 answer

If you sort your gff file by chromosome and start position you could do the following in bash:

cat file.gff | awk -F'\t' '$3=="CDS"' | grep {protein_id} -A 2 -B 2

Hope this helps.

• 0 views • link
updated by SES SES • written by Raygozak Raygozak

Really nice and simple approach!

• 0 views • link
written by PoGibas PoGibas

I am working with EMBL files.

• 0 views • link
written by Pappu Pappu

Log in to answer this question.

More posts like this