Exonerate and Genetic Code

[Natacha]

Hello,

I used exonerate since 2 years (version 1.4), in particular the
prot2genome model, in order to define the locations of introns.

I test the new version (2.2) of exonerate.
The options --splice3 and --splice5 for change the splice score matrix
works perfectly.

But I have problem with the option --geneticcode !! When I used the
following command :

exonerate --model protein2genome --useaatla F --minintron 142 --
intronpenalty -35 --geneticcode 1 Desktop/prot Desktop/gene
> result_with_geneticcode1

I obtain the result in file result_with_geneticcode1.

And when I used the following command :

exonerate --model protein2genome --useaatla F --minintron 142 --
intronpenalty -35 --geneticcode 4 Desktop/prot Desktop/gene >
result_with_geneticcode4

I obtain the result in file result_with_geneticcode4.

The result is same for the two commands, or for the second command the
codon TGA must be code for W and not for stop.

I don't understand my mistake. Somebody use exonerate with genetic
code ? And can help me ?

Thanks for your help.

Natacha.

[Fred]

Hello Natacha,

No clue for your problem but a suggestion : Did you try to contact the
Guy Slater, cited in the about section of the exonarate webpage.
He seems to be the right person to fix your problem since he works on
this package.

Hope this helps.

Fred

[Natacha]

Hello Fred,

Thanks for you help and your suggestion.
I will send him an e-mail.

Natacha