[Bioperl-l] Re: translation using Bioperl

[Heikki Lehvaslaiho]

Dear Jonathan,

Thanks for persisting. I learned something new. (I had to check it
with a
couple of experts before I believed!)

To summarize: The amino acid that starts a polypeptide in translation
process is always methionin, even if an alternative initiator codon is
used. That means that even when using the standard codon table, the
correct translation of the sequence 'AGT TGA ...' is 'MV...'.

I've fixed this in bioperl live and 06 CVS branches.

If you want to catch those cases where translation is NOT started by a
valid initiator codon, you can now set ->verbose to true in your
PrimarySeq object and it will warn you.

	-Heikki

"Lin, Xiaoying Jonathan" wrote:
> 
> Dear Heikki,
> 
> Thanks for the reply. The problem I encountered was exactly with the
> alternative initiator codons.
> The codon 'CTG', when at initiator position, should encode 'M' not 'L'
> according to GenBank.
> 
> http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c#SG11
> 
> I am wondering if your module translate those GUG, UUG, AUU, CUG at first
> codon into 'M'?
> If not, whether there should be a flag to set to do so....
> 
> Thanks for the help and bioperl.
> 
> --X. Jonathan Lin  || Celera Genomics/Chrom Team || 240-453-3695
> 
> > -----Original Message-----
> > From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk]
> > Sent: Tuesday, July 25, 2000 4:53 AM
> > To: Lin, Xiaoying Jonathan
> > Subject: Re: translation using Bioperl
> >
> >
> >
> > Dear Jonathan,
> >
> > The program works as it should. The bacterial codon table 11 is in
> > fact identical to 1 except that is defines several new alternative
> > initiator codons:
> >
> > http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi?id=11&Action=Show
> >
> > The reason for this confusing state of affairs is that these codon
> > tables have been devised to give slightly simplified taxonomic view of
> > translation machinery in all living organisms. Have a look at the  the
> > NCBI Genetic Codes home page for more details:
> >
> > http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
> >
> > Yours,
> >
> >       -Heikki
> >
> > P.S. I'll add a comment on this into CodonTable.pm
> >
> > "Lin, Xiaoying Jonathan" wrote:
> > >
> > > Hi,
> > >
> > > I am having a problem when using your module to translate a
> > microbial gene.
> > > With codon table 11
> > > The script I wrote will pass the codon_table_id 11 to the
> > your 'translation
> > > method', but what I got back is from still the standard default.
> > > I am not sure what I did wrong.   Could you help?
> > >
> > > Thanks very much.
> > >
> > > --X. Jonathan Lin  || Celera Genomics/Chrom Team || 240-453-3695
> > >
> > > #!/usr/local/bin/perl
> > >
> > > # my translation, a free stand tool
> > > # mytrans <condon tableid> <fastafile>
> > >
> > > use lib "/work/chrom/users/linxj/lib/local_pm/";
> > >
> > > use Bio::SeqIO;
> > > use Bio::PrimarySeq;
> > >
> > > $codon_tblid= $ARGV[0];
> > > $myfile = $ARGV[1];
> > >
> > > $seqio  = Bio::SeqIO->new ( '-format' => 'Fasta' , -file =>
> > $myfile);
> > >
> > > while ($seqobj = $seqio->next_seq()) {
> > >     $aaobj = $seqobj->translate('*', 'X', 0, $codon_tblid);
> > >
> > >     $len = $aaobj->length();
> > >     $seq = $aaobj->seq();
> > >
> > >     print ">" . $aaobj->id ."\n";
> > >     for ($i=0; $i< $len; $i+= 60) {
> > >         print substr($seq, $i, 60),"\n"; #
> > >     }
> > > }
> > >
> > > __END__
> > >
> > > cat cds
> > >
> > > >cds
> > >
> > CTGAATAAAAAGAAGACGCTGTACTTTGGTGCCGGTTGGTTTAATGAAAAGCAAAACAAAGCTTACAAAG
> > >
> > AAGCAATGGCAGCTTTAAAAGAAAATCCAACAGTTGATTTAGAAAATAGTTATGTGCCCCTTGAAAACCA
> > >
> > ATACAAGGGTATTCGCATTGATGAGCATCCACAGTACTTGCACAACATTGAATGGGCTTCTGCAACCTAC
> > >
> > CACAATGATTTAGTAGGAATTAAGACTTCTGATGTCCTGCTTGGCGTATATCTGCCACAAGAAGAACACG
> > >
> > TCGGCTTAGGCATGGAACTGGGCTACCCATTATCTCAAGGAAAATTATTTTTTTGGTTTTCCCATATGAA
> > >
> > AGATTACGGCAAGCCAATCATCTTAATGAGCTGGGGCGTTTGTGACAATGCCAGTCAGATCAGTGAATTA
> > > AAAGACTTCGACTTTAACAAGCCTCGCTACAATTTCTACGACGGAGCTGTATATTAA
> > >
> > > linxj@chmap (82) mytrans 11 cds
> > > >cds
> > > LNKKKTLYFGAGWFNEKQNKAYKEAMAALKENPTVDLENSYVPLENQYKGIRIDEHPQYL
> > > HNIEWASATYHNDLVGIKTSDVLLGVYLPQEEHVGLGMELGYPLSQGKLFFWFSHMKDYG
> > > KPIILMSWGVCDNASQISELKDFDFNKPRYNFYDGAVY
> >
> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
> >

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________