[Bioperl-l] TGA as U in selenocystine fullCDS

[Albert Vilella]

On Fri, 2005-02-18 at 11:28 +0000, Heikki Lehvaslaiho wrote:
> Albert,
> 
> The best way to deal with this would be to have genetic code that correctly 
> translates into selenocysteine. Unfortunately I could not find anything on 
> the topic on Taxonomy Genetic codes home page: 
> <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>.
> I guess I should ask around if there are plans to deal with this.
> Are those CDSs from EMBL or Genbank? If so, could send me a few accession 
> numbers to check.

from Genbank:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=57016379


> The translate method has already too many optional arguments, so rather not 
> put in any more solely for dealing with celenocysteine.

True.

> 
> Could you put together (and send to me) data lines for @NAMES, @TABLES and 
> @STARTS in Bio::Tools::CodonTables and call it tentatively "Standard with 
> celenocystein" and use id 20 which has been merged with existing codes and 
> not currently in use. That should provide a working code for your purposes 
> while I try to find a consensus on this.

I have added a "Standard with selenocysteine" in 20.
I have also added a "Bacterial with selenocysteine" in 19.

Now is not apparent that 20 and 19 are only for in-frame TGAs, not codon
stops in CDSs. 

I've seen an email from Ewan in 2004-July bioperl-ml that they solved
that problem in ensembl, but I haven't found how they did it in their
code:

http://portal.open-bio.org/pipermail/bioperl-l/2004-July/016363.html

    Albert.

**************

    @NAMES =			#id
	(
	 'Standard',		#1
	 'Vertebrate Mitochondrial',#2
	 'Yeast Mitochondrial',# 3
	 'Mold, Protozoan, and CoelenterateMitochondrial and
Mycoplasma/Spiroplasma',#4
	 'Invertebrate Mitochondrial',#5
	 'Ciliate, Dasycladacean and Hexamita Nuclear',# 6
	 '', '',
	 'Echinoderm Mitochondrial',#9
	 'Euplotid Nuclear',#10
	 '"Bacterial"',# 11
	 'Alternative Yeast Nuclear',# 12
	 'Ascidian Mitochondrial',# 13
	 'Flatworm Mitochondrial',# 14
	 'Blepharisma Nuclear',# 15
	 'Chlorophycean Mitochondrial',# 16
	 '', '',  '',
         'Bacterial with selenocystein', # 19
         'Standard with selenocystein', # 20
	 'Trematode Mitochondrial',# 21
	 'Scenedesmus obliquus Mitochondrial', #22
	 'Thraustochytrium Mitochondrial' #23
	 );

    @TABLES =
	qw(
	   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
	   FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   '' ''
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
	   FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
	   FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   '' ''
	   FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
	   FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	   );


    @STARTS =
	qw(
	   ---M---------------M---------------M----------------------------
	   --------------------------------MMMM---------------M------------
	   ----------------------------------MM----------------------------
	   --MM---------------M------------MMMM---------------M------------
	   ---M----------------------------MMMM---------------M------------
	   -----------------------------------M----------------------------
	   '' ''
	   -----------------------------------M----------------------------
	   -----------------------------------M----------------------------
	   ---M---------------M------------MMMM---------------M------------
	   -------------------M---------------M----------------------------
	   -----------------------------------M----------------------------
	   -----------------------------------M----------------------------
	   -----------------------------------M----------------------------
	   -----------------------------------M----------------------------
	   '' ''
	   ---M---------------M------------MMMM---------------M------------
	   ---M---------------M---------------M----------------------------
	   -----------------------------------M---------------M------------  
	   -----------------------------------M----------------------------
	   --------------------------------M--M---------------M------------
	   );

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