[Bioperl-l] About bioperl global alignment

[Frank Schwach]

Hi Prasad,

have a look at this:
http://www.bioperl.org/wiki/HOWTO:AlignIO_and_SimpleAlign#Aligning_multiple_sequences_with_Clustalw.pm_and_TCoffee.pm

The HOWTO pages are a brilliant source of information and starting 
points for your own scripts.
The main point here is: Bioperl doesn't do any alignment. It provides 
the tools to automate making alignments (or other things) with 
third-party software such as ClustalW or TCoffee as described in the 
text. You need to install those programs locally and then use Bioperl to 
go fetch sequences form your FASTA (or whatever format) sequence files 
and run them through the aligner, then use more Bioperl methods to 
extract data from the alignments and generate your final results. That 
makes it possible, for example, to write a script that extracts every 
possible pair of sequences from a FASTA file and run them through 
ClustalW, then analyse the results and record the percent identity or 
whatever you are interested in and generate a spreadsheet with your 
final results, ready to be sent to Nature :-) !!!! Feel free to ask if 
you need more help.

Good luck!

Frank


On 04/05/12 06:13, Prasad ms wrote:
> Hello sir,
> I am Prasad, student of MS in bioinformatics. I am doing my final year
> project, and sequence alignment is the part of my project. I am having
> nearly 50k sequences and i want to do a pairwise global alignment (NW
> alignment). I read the bioperl tutorial. But in that there is no mention
> about this. Could you please guide how can i do this type of alignment
> using bioperl.
> I assure that all the usage is purely for academic.
>
> Looking forward  to hear from you.
>
> Thank you,
>
> Regards,
> Prasad MS
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> Bioperl-l at lists.open-bio.org
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