[EMBOSS] backtranseq

[Andres Pinzon]

This is a not too elegant solution to your problem:
paste the following code in a file called "script.sh":
======================================


#!/bin/bash

        seqret -ossingle -sequence $1 -outseq 1.fasta


        for i in $( ls ); do
                if [ "$i" != "script.sh" ]; then
                        echo Processing: $i
                        backtranseq -sequence $i -outfile $i.bt
                fi
        done

        cat *.bt > $1.backtranslated.fasta

=================================================

and run the script as this:
==================================================
./script.sh    ../yourMultipleFastaFile
==================================================


This script will take your multiple fasta file, will create single
files from it. will run backtranslate on each of them and will create
an output file with your results called:
yourMultipleFastaFile_backtranslated.fasta


Hope it helps.

regards,



On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
> Magdy Alabady wrote:
>>
>> Hello all,
>>
>> Can backtranseq run input file contains several 100's of protein sequences
>> in Fasta format? can it make bulk back translation? please tell me how to
>> do
>> so if it is possible
>
> Backtranseq only processes a single sequence. You have several choices:
>
> 1. make a new version of backtranseq that can process multiple sequences
> (easy to do ... but you need to learn a little EMBOSS programming first :-)
>
> 2. put your sequence file in a directory and name it with anything other
> than a .fasta extension.
>
> use seqret -ossingle to convert your file into 100s of single sequence files
>
> run backtranseq on each of the individual files.
>
>
> I wonder ... do you really want 100s of backtranslations in a single file?
>
> regards,
>
> Peter Rice
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>



-- 
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