in reply to How do I extract ORFs from a fasta file into a new fasta file

"I would like to pull out all of the full length CDS with some 5' and 3' UTR info for the proteins I have found in the tissue by mass spec"

If I understand you correctly, I will look at the gff/gtf coordinates for the CDs feature and try to obtain that for the specific protein annotation in the gff file, A fastA file may not have these features handy so it maybe not the way to go unless you have an annotated genome somewhere for you to extract this stuff from.

"I have tried simply blasting the peptides against the assembly but I get hits that are not in open reading frames"

Maybe because BLAST is a local alignment and search tool, that behavior is totally expected.

" I would suppose the major difference is that I need to return all the ORFs from tens of thousands of entries as a new fasta file."

Read the file one line at a time. Maybe something like what follows ?... If you don't have BioPerl installed then certainly there are many other examples on reading fastA file that don't use BioPerl around here

#UNTESTED CODE TO DEMONSTRATE A WAY AROUND use strict; use warnings; use Bio::SeqIO; my $in = Bio::SeqIO->new(-file =>"FastA.fa", format = "FASTA"); while(my $seq = $in->next_seq){ my $sequence = $seq->seq; #Do something with $sequence my $ORFpattern = "foo"; if($sequence =~ /$ORFpattern/){ #report or anything } }

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