Hi Pearl Monks. In short: I am a Biochemistry Ph.D. student working on a proteomics project. I am new to programming and Perl. I have an assembled RNA-seq fasta file and I need to extract all of the ORFs into a new fasta file that I can use to blast proteome data against. Any advice on how I can proceed would be very appreciated.

The long story: The RNA-seq data I have is a de-novo assembly of illumina data without a reference genome. This file is far to long to open it on my computer let alone go through it by hand. I also have some mass spec data that returned tryptic peptide sequences from the same tissue. 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. I have tried simply blasting the peptides against the assembly but I get hits that are not in open reading frames. It is my hope that if I have a database of only ORFs that identification of my peptides transcripts would be easier. I have read Borisz answer to a similar question in node id=473744 back in 2005. I have copied his code below. I believe this is a good place to start, but 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. Thank you for your consideration. 
local $_  = $your_input_string;
while ( /ATG/g ) {
   my $start = pos() - 3;
   if ( /T(?:AA|AG|GA)/g ) {
     my $stop = pos;
     print $start, " ", $stop, " ", $stop - $start, " ", 
       substr ($_, $start, $stop - $start), $/;     
   }
}

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In reply to How do I extract ORFs from a fasta file into a new fasta file by Wasp_Guy

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