[Bioperl-l] query

[Mane, Ajay (UMR-Student)]

Hi,

I am Ajay from University of Missouri - Rolla, doing research in
bioinformatics. The bl2seq tool takes 2 sequences to align. I am
interested in a list of sequences and want to compare them. Instead of
putting 2 at a time, I have a large list of pairs to be analysed. How do
I automate the process. Everytime running the tool and manually looking
for the point where the coding of proteins start is time consuming. Can
I write a perl file to automate the process. Can I get any help on this.
I have gone through the bioperl modules, but could not find on bl2seq. 

Thanks,
Ajay