blasting for proteins using NCBIWWW in a specific organism
does anyone know how to use NCBIWWW to blast for proteins in one organism? I am trying to find a set of proteins in the fish, Fundulus heteroclitus.
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Breilly92 •
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On the blast page (e.g. blastp) under the section "Choose search set" enter the name of your organism in "Organism" box (Fundulus heteroclitus (taxid:8078). The page does automatic name lookup as you start typing in the box.
Edit: Re-reading your question it sounds like you are asking if it is possible to find proteins from this fish using blast as a general tool. Use a sequence from a related organism (or another fish) with www blast in that case.
If you just need all proteins from this fish that fasta file is here.
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Is there a way to write that in to a program?
You could use the protein file I linked below to create a custom blast database and use that on the command line.
thank you very much this really helped