Sorry if this seems like a naive and simple question. I have the whole genome of my species as a fasta file and a file containing a list of protein IDs. What is the easiest way to get a file that contains the fasta sequence for each of the proteins in the second file?
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What species?
If it is one of the common genomes NCBI is likely to have the protein fasta file available. -
I can get the protein fasta file. It's more the extracting the sequence for my specific list of protein IDs that I'm struggling with.
It is the monarch butterfly so not a particularly common species.Comment
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Look into faSomeRecords utility from Jim Kent: http://hgdownload.soe.ucsc.edu/admin.../faSomeRecords I have provided linux link but OS X/Source code is also available at the site.
Provide the list of ID's to faSomeRecords and it will extract the fasta sequence for your ID's, which you can save to a new file.Comment
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