Getting Names Of Proteins Around A Protein In A Genome

Question

[Pappu]

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.

[Neilfws]

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.

Answer 1

[Raygozak]

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.

[PoGibas]

Really nice and simple approach!

[Pappu]

I am working with EMBL files.