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

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

biopython command-line blast+ parsing
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updated by Peter Peter • written by jcastrofigueroa jcastrofigueroa

2 answers

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

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written by Khader Shameer Khader Shameer

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?

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written by jcastrofigueroa jcastrofigueroa

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.

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written by Peter Peter

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