[Bioperl-l] Re: About reverse translation

[Todd Naumann]

Jian,

Searching for Drosophila melanogaster at www.kazusa.or.jp/codon gives 4 
possible tables. I think that your program is picking the genome usage 
table by default. If this is what you want I think you are in business. 
I am not sure how to specify if you want 1 of the others. With 
Escherichia coli I was able to specify by simply adding the 'K12'. In 
your case I tried to specify 'mitochondrion Drosophila melanogaster' or 
'Drosophila melanogaster mitochondrion' but always get an error and the 
program defaults to Homo sapiens.

-Todd

On Sep 27, 2004, at 10:59 AM, Sun, Jian wrote:

> Thanks a lot. Todd. While accroding to the CodonUsage table, I still 
> have a question. For example, I want to use the Drosophila 
> melanogaster codonUsage table, (its corresponding genetic code table 
> is, id=>5). From the site-www.kazusa.or.jp./codon/, I get the species 
> name  for 'Drosophila melanogaster' ($organism = "Drosophila 
> melanogaster") and tried the program. And a warning message shows as 
> below:
> -------------------------Warning----------------------------------
> MSG: too many species - not a unique species id - .......
> -------------------------------------------------------------------
> The how can get the unique species id?
>
> Thanks a lot
> Jian Sun
> University of Texas at Dallas
>
>
> ________________________________
>
> From: Todd Naumann [mailto:tan10 at psu.edu]
> Sent: Fri 9/24/2004 2:52 PM
> To: jsun at utdallas.edu
> Cc: bioperl-l at portal.open-bio.org
> Subject: Re:About reverse translation using.....
>
>
> Jian,
>
> The following program takes a species, genetic code i.d., and peptide 
> sequence as input. It then retrieves data from the web using 
> Bio::DB::CUTG to create a Bio::CodonUsage::Table object. (Check out 
> www.kazusa.or.jp./codon/ to find correct species name to use, for E. 
> coli there are several). I then use Bio::Tools::CodonTable to do the 
> reverse translation and Bio::CodonUsage to determine which of the 
> codons is most frequent. The output is then the oligo sequence 
> matching the given peptide using the most frequent codons. I think 
> this or something similar is what you are trying to do. If not maybe 
> it will help put you on the right track.
>
> -Todd
>
>
> #!/usr/bin/perl
>
> use strict;
> use warnings;
> #use lib "/Users/todd/.cpan/build/bioperl-1.4";
> use Bio::CodonUsage::Table;
> use Bio::DB::CUTG;
>
> my $organism = "Escherichia coli K12";
> my $gc = "11";
> my $amino_acids = "AKLMG";
> my @peptide = split //, $amino_acids;
> my $oligo;
>
> # get a codon usage table from web database
> my $db = Bio::DB::CUTG->new(-sp => $organism,
> -gc => $gc);
> my $CUT = $db->get_request(); # This is Bio::CondonUsage::Table object
>
> # use Bio::Tools::CodonTable to do the reverse translation
> # with a specified table
> my $CodonTable = Bio::Tools::CodonTable->new(-id => $gc);
>
> # Loop throught the amino acids and pick most frequent
> # codon
> foreach (@peptide) {
> my @possible_codons = $CodonTable->revtranslate($_);
> my $most_frequent = shift @possible_codons;
> foreach my $next_codon (@possible_codons) {
> if ($CUT->codon_rel_frequency($next_codon) > 
> $CUT->codon_rel_frequency($most_frequent)) {
> $most_frequent = $next_codon;
> }
> }
> $oligo .= $most_frequent;
> }
> print "The DNA sequence is: $oligo.\n\n";
> exit;
>
>
> Todd Naumann
> Post-Doc, Stephen Benkovic lab
> Dept. of Chemistry
> Penn State University
> University Park, PA 16801
>
>