[Bioperl-l] parsing BLASTX

Sean Davis sdavis2 at mail.nih.gov
Wed May 19 23:49:49 EDT 2004


Yes, you do need to write your own scripts.   However, there are numerous
examples out there.  I suggest that you literally copy the script from the
HOWTO and change the filename to one that you have generated.  Save the file
as blastparseexample.pl and execute it using:

perl blastparseexample.pl

It will print out the information that you ask (i.e., you will have to
change the blastparseexample.pl file to your own liking).  The table in the
HOWTO shows you what information from the blast report maps to what bioperl
method.  It isn¹t complicated, but you have to start with a working example
before you can experiment.


On 5/18/04 6:00, "Javier Terol" <jterol at ivia.es> wrote:

> Hi!
> I am an absolute begginer in the use of perl and bioperl modules. I am
> interested in parsing a flile resulted from BLASTX. I have installed the
> Bio:SearchIO modules, but after reading the HOWTO I did no get a clear idea
> about what to do. Am I supossed to write my own scripts? How can I run the
> SearchIO modules?
> I would appreciate very much a step by step "protocol" for parsing the blastx
> file, from the begining.
> Thank you very much in advance.
> Javier
>   O@@@@@       
>  @@@O@@O@      Javier Terol Alcayde
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