and geneticcode database ?

Heikki Lehvaslaiho heikki at ebi.ac.uk
Tue Nov 17 09:42:55 EST 1998


Guy Bottu wrote:
> 
> : I still only get 6 codes linked. I used the taxonomy file
> : ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
> 
> That is because the taxonomy.i file at the EBI contains some error. To
> convince yourself of this, search in taxonomy the taxon "homo sapiens"
> and link to geneticcode, you will see that you find only "Vertebratrate
> Mitochondrial" and not "Standard". The cause of the problem is that the
> link from taxonomy to geneticcode is defined twice.
> 
>         Guy Bottu


I've corrected a number of errors. The link is now performed only once
and link keys are read from a new token table created by production
called l_gencode. Since links are created from taxonomy to geneticcode,
the taxonomy files change again. Sorry, Peter!


The previous version of gc.prt file contained the IDs 13-15 so I copied
them from there into a new file and put it into EBI FTP site:

	ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/

I've informed NCBI about the problem.


After this the only codes that are not referenced by taxonomy database 
are:

Query "geneticcode! (taxonomy>geneticcode) " found 2 entries 

id 7	Protozoan Mitochondrial (and Kinetoplast)
id 8 	[OBSOLETE, posttranscriptional editing only] Plant
		Mitochondrial/Chloroplast


It's all yours to play with now. Have fun,

	-Heikki

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