How Can I Record A Specific Domain Sequence Within A Protein Query?

Question

[jcastrofigueroa]

Hello everyone: I'm just beginning with massive search on my own database of proteins and I need some guidelines to start. What I'm trying to do is recording (as *.fasta file) a specific domain sequence within a protein sequence from a large database of proteins. Any suggestion to begin?

Thanks

JFC

Answer 1

[Khader Shameer]

You can consult a protein domain database that already provides domain specific sequence information.
See: Pfam, CDD, SMART or InterPro

[jcastrofigueroa]

OK! Thanks.

I'd like to use RPS-BLAST to search for specific domains on my own database of proteins using the CDD database, in my computer. Then, I'd like to record or save the sequence of a domain, within my protein, that matches with a conserved domain. Is it possible using standalone RPS-BLAST?

Answer 2

[Peter]

Have a look at UniProt for how they annotate their protein collection, available as XML files and plain text "SwissProt" files, plus other formats like JSON and RDF.