[Bioperl-l] Re: translation using Bioperl

Ewan Birney birney@ebi.ac.uk
Tue, 25 Jul 2000 16:38:53 +0100 (GMT)


On Tue, 25 Jul 2000, Heikki Lehvaslaiho wrote:

> 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 - 

Can we watch the ->verbose attribute. This will have to be in on
Bio::PrimarySeqI --- and i would prefer we did not burden other
implementations with having to set this.


Would it be ok to let translate (optionally) take a verbose argument on 
the function call?




 > 
> 	-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
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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