[Bioperl-l] PAML + Codeml problem..

[Albert Vilella]

I added a couple of custom tables with selenocystein in my local copy a
while ago, but never commited the change to the CVS.

Again, this doesn't solve how codeml deals with it, but one can always
change the selenocysteine triplets with "NNN" before running codeml...

207,209c207
<        '', '',  '',
<          'Bacterial with selenocystein', # 19
<          'Standard with selenocystein', # 20
---
>        '', '',  '', '',
215,220d212
< # Bases at each position are:
<
< #-- Base1
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
< #-- Base2
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
< #-- Base3
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
<
238,241c230,231
<          '' ''
<
FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
<
FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
<
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
---
>          '' '' '' ''
>
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
264,266c254
<          '' ''
<
---M---------------M------------MMMM---------------M------------
<
---M---------------M---------------M----------------------------
---
>          '' ''  '' ''
355,377d342


On Mon, 2006-08-14 at 17:22 -0500, Chris Fields wrote:
> Brian,
> 
> Would having a custom codon table work?  Since TGA->'U' requires a nearby
> SECIS element, theoretically a gene could have one 'TGA' codon that codes
> for 'U' (nearby SECIS element) and another 'TGA' codon that codes for the
> actual stop (no SECIS element).
> 
> I don't think there is a way to have position-specific TGA->U based on
> user-input either (a flag, perhaps).  That's the only work-around for it I
> can think of.
> 
> Chris
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Brian Osborne
> > Sent: Monday, August 14, 2006 4:49 PM
> > To: Xianjun Dong
> > Cc: bioperl-l at lists.open-bio.org; aaron.j.mackey at gsk.com;
> > golharam at umdnj.edu
> > Subject: Re: [Bioperl-l] PAML + Codeml problem..
> > 
> > Xianjun,
> > 
> > I spoke too soon. I'd assumed that NCBI had a table to handle
> > selenocysteine, but it does not:
> > 
> > http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
> > 
> > These tables are the basis for the Bio::Tools::CodonTable module, and the
> > CodonTable module looks to be up-to-date with respect to NCBI's page. You
> > can solve your problem by making a custom table using the add_table()
> > method, see t/CodonTable.t for a nice example. Your custom table will look
> > something like the Euplotid Nuclear Code table, which translates TGA to C.
> > You should be able to translate TGA to U since the amino acid codes that
> > CodonTable inherits from Bio::SeqUtils contain "U" and "Sec".
> > 
> > This is an issue that's independent of the issue raised by Aaron, I'm
> > assuming you know whether or not your sequences should be translated this
> > way.
> > 
> > Brian O.
> > 
> > 
> > On 8/14/06 3:11 PM, "aaron.j.mackey at gsk.com" <aaron.j.mackey at gsk.com>
> > wrote:
> > 
> > >>> 1. For the case which in-frame stop codon codes for
> > > selenocysteine('U'),
> > >>> like the transcript ENSMUST00000094469, it should be translated into
> > >>> 'U', not '*' since the IUPAC/IUBMB has officially recommended it. But
> > >>> when I use the codontable_id=1(generic codon table), it still was '*'.
> > >>> Is it because the package(Bio::Tools::CodonTable) is not so updated as
> > >>> the IUPAC rules?
> > >
> > > The translation of TGA into Selenocysteine (U) is not "universal", it
> > only
> > > occurs when the downstream UTR contains a SECIS RNA element;
> > > Bio::Tools::CodonTable is unable to differentiate such
> > > selenocysteine-encoding TGA codons from "normal" TGA stop codons,
> > > regardless of the translation table in use.  GenBank/EMBL-formatted
> > > records will typically have /transl_except entries in the feature table,
> > > but the BioPerl "translate" method does not (yet) recognize these
> > (someone
> > > correct me if I'm wrong).
> > >
> > > -Aaron
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
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