[EMBOSS] recursive backtranslate

Andres Pinzon andrespinzon at gmail.com
Fri Mar 13 15:29:53 UTC 2009

Hi all,
thank you for your answers,
Just in case anyone could need it, this is a small bash script which
does the job:

LIST=`ls *.fasta`
for i in $LIST
        backtranseq -sequence $i -auto

First run seqretsplit on your multiple fasta file,  and run this
script from  the directory where your fasta files were stored.


On Fri, Mar 13, 2009 at 5:30 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
> david.bauer at bayerhealthcare.com wrote:
> emboss-bounces at lists.open-bio.org schrieb am 13/03/2009 01:13:15:
>> > 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.
>> it just takes one sequence as input.
>> 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.
> We have already extended backtranseq for the next release to work over
> multiple sequences.
> The changes needed are not difficult if you want to try a little
> programming.
> regards,
> Peter Rice

Andrés Pinzón
Bioinformatics Center, Colombia EMBnet node
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768

More information about the EMBOSS mailing list