Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
Thu Oct 18 08:40:55 EDT 2001
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
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 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
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