[EMBOSS] recursive backtranslate

[david.bauer at bayerhealthcare.com]

Hi Andrés,

it just takes one sequence as input.

Btw. you can see this if you look what the emboss programs say with -help.

> backtranseq -help
   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   (Gapped) protein sequence filename and
                                  optional format, or reference (input 
USA)

If it says "sequence" than it takes just one sequence as input.

> infoseq -help
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and 
optional
                                  format, or reference (input USA)

If you see "seqall"  than the program can work on more than one sequence.

For your problem you can either use "seqretsplit" to split up our file 
into individual sequences or you can write a script which iterates through 
the multiple fasta file with "skipseq" and sends its output to 
backtranseq. 

Cheers,
David.


emboss-bounces at lists.open-bio.org schrieb am 13/03/2009 01:13:15:

> Hi everyone,
> Is it possible to give backtranseq a muliple fasta file as input and
> have all the sequences in it translated?
> I have tried several times but backtranseq  backtranslates just the
> first sequence of my multiple fasta file.
> 
> best,
> 
> -- 
> Andrés Pinzón
> http://bioinf.ibun.unal.edu.co/~apinzon/
> Bioinformatics Center, Colombia EMBnet node
> http://bioinf.ibun.unal.edu.co
> Tel +57 3165000 ext 16961 Fax +571 3165415
> Micology and Phytopathology Laboratory - Los Andes University.
> http://bioinf.uniandes.edu.co
> Tel +571 3394949 ext. 2768
> 
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