[EMBOSS] Translate and convert start codon to Methionine

[Peter Rice]

Dear Stefanie,

On 24/01/2013 05:43, Stefanie Lager wrote:
> Hi,
>
> Is there ANY Emboss program that can translate DNA sequence and
> convert the different possible start codons to methionine correctly?
> Transeq doesn't seem to be able to do it, getorf is supposed to be
> able to do it but the -methionine Y option doesn't seem to work?

You need to set a couple of options in getorf,

Note that -methionine is already on by default, you can set  it to 'N' 
or use -nomethionine to turn off the conversion of start codons in getorf.

You have to use a genetic code table with alternative starts, for example:

-table 1

uses an alternative genetic code with atg, ttg and ctg as starts, or:

-table 11 uses more alternative starts for bacteria and chloroplasts

You may need to set the '-find' option. Getorf assumes the sequence is a 
fragment, so all ORFs are already open until a stop codon is reached.

-find 1

requires a start codon in the sequence to open an ORF. If the start 
codon you are looking for is in an already open reading frame this may 
be the option you need to translate it as methionine.

Hope this helps

Peter Rice
EMBOSS Team