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.
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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version 2.3.6
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