getorf

[Gary Williams, Tel 01223 494522]

Michael Behnke wrote:
> 
>   I have been using the getorf program recently to find ORF's in
> Cryptosporidium contigs with great results.  I do have a question though.
> Does anyone know what are the STOP and START codons used by the program,
> and do they change depending upon the table one uses?  I see that plotorf
> uses Stop codons = TAA,TAG,TGA and Start codon = ATG, are these the same
> for getorf?

Yes, the STOP & START codons are held in the genetic code tables and
will change with the table you choose.

By default this is the Standard Code
(See http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c)

The STOP & START codons in the default table are, as you describe above, 
Stop codons = TAA,TAG,TGA and Start codon = ATG.

The '-table' qualifier allows you to pick other tables.

Gary

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK