Search The Protein Domain By Sequence In Batch Work

Question

[camelbbs]

Hi all,

I want to ask if there has some good tools to search the protein domain by sequence and can work as batch input, eg. 1000 hits.

I have some genomic coordinates. All of them are from exon region, we can treat it as coding region.

       chr16    68355366    68355614
       chr9    71081078    71081471
       chr11    77611818    77611831
       chr5    139645292    139645415
       chr14    105693098    105694607
       chrY    22748604    22749732

After I get the DNA sequence, I translate it to protein sequence. There will have 6-frame translation so there will be 6 results for each exon.

Then I need to search if there is any special domain, eg. zinc finger domain in this exon.

Any good suggestions for this process?

Thanks a lot!

Answer 1

[David Westergaard]

The only actual question I can derive from your post is "How do I search a protein sequence for functional/structural regions?". Pfam and Interpro were designed for this specific purpose. Both provide commandline scripts which allows you to search as many genes as you want. The computational time is also almost as efficient as BLAST. Results are, however, much easier to interpret.

[camelbbs]

Thanks for the suggestion!