Codon Usage 25 for bacteria

[Aurélie Génin Lajus]

Dear Contributor,

I am Ms. Aurélie Génin, bio-computer scientist at the CEA in Evry and developer on MicroScope platform. We use prodigal to CDS prediction of bacterial genomes.

We encounter a problem. We have some bacterial genomes using the genetic code 25 but your program does not take into account.

Is it possible that in a future version, this is the case and when.

In advance thank you very much.

Aurélie

25. Candidate Division SR1 and Gracilibacteria Code (transl_table=25)

    AAs  = FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ---M-------------------------------M---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

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Differences from the Standard Code:

          Code 25        Standard

UGA       Gly            STOP *

Initiation Codons:

AUG, GUG, UUG

Systematic Range:

Candidate Division SR1, Gracilibacteria

Comments:

Code 25 is used in two groups of (so far) uncultivated Bacteria found in marine and fresh-water environment and in the intestines and oral cavities of mammals among others. The difference to the standard and the bacterial code is that UGA represents an additional glycine codon and does not code for termination (Campbell et al. 2013).

[dhyatt1]

Hi,

I've added support for translation table 25 to the latest source commit at github.  Going to test for a few days and make sure everything is ok before releasing a 2.6.2.

regards,

doug