Getting sequences from multiprotein .faa file?

[ewilbanks]

Anyone have a favorite command-line method for grabbing specific entries from a FASTA Amino Acid (.faa) file? I have a list of sequences that I'd like to pull out of a larger file. I usually use mothur's get.seqs() for this kind of fasta processing but it can't handle protein sequences.

Cheers,
Lizzy

[ewilbanks]

Found a nice solution to this - in case anyone's ever looking...

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64.v287/faSomeRecords

[yzzhang]

Yes, I use fasomeRecords a lot, and it works very well

[Wallysb01]

Just you the blast toolkit.

You can just format your database (amino acid or nucleotide) with makeblastdb then use blastdbcmd to pull things out by gene name. It can take a batch mode from an input file with sequence names or single sequences specified on the command line.

[maubp]

Galaxy solutions:

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/