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Re: translating multiple DNA sequence to protein sequence

by polypompholyx (Chaplain)
on Aug 19, 2013 at 11:16 UTC ( #1050014=note: print w/ replies, xml ) Need Help??


in reply to translating multiple DNA sequence to protein sequence

If you're planning on using Perl for bioinformatics, you might be better off installing BioPerl rather than hand-rolling FASTA parsers and translation codon tables.

use Bio::SeqIO; my $sequences = Bio::SeqIO->new( -file => "sequence.fasta", -format => "fasta", ); while ( my $dna = $sequences->next_seq ){ my $protein = $dna->translate( -codontable_id => 1, # standard genetic code -frame => 0, #reading-frame offset 0 ); print $dna->display_id, "\n"; print $protein->seq, "\n\n"; }
Having said that, installing BioPerl (1.6.901) on Windows seems to be more difficult than I was expecting: I had to resort to force with Strawberry and CPAN, having simply given up trying to get it to install with ActivePerl and PPM.


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