[EMBOSS] how to get jtranslations using extractfeat?

[Peter Rice]

Andres Pinzon wrote:
> Hi,
> Im trying to get all the "/translation" sequences from a genome embl
> feature file.
> I mean, each CD have a translation tag and I need those translations
> in a fasta file. I've tried all possible combinations of  -type -tag
> but i can not get the translated sequences, but the DNA sequences.
> 
> Is it possible to get this translated sequences from the feature file?
> Or do I have to get the corresponding CDS DNA sequences and then translate them?

Good suggestion ... we can try to make a new application. The /translation tag 
is rather special (because the value is a real sequence) ... also it may have a 
different name in some databases or feature file formats.

We will need to make up names for each translation (sequence identifiers, and 
something derived from the feature table) like the names used by extractfeat.

Alternate splicing will make it difficult to create reliable unique names. 
Extractfeat does have the same problem - and nobody has complained. If we keep a 
table of names so far we can add something to the end of any duplicates.

Extracttrans is a possible name for the program.

regards,

Peter