[Bioperl-l] Module for secondary structure feature recognition ?

[Goel, Manisha]

Hi All,

I am new to list as well as Bioperl, with some experience with perl.


I need a perl script that does the following:

I have  a multiple sequence alignment, from which I want to extract
blocks of alignment. This can possibly be taken care of easily by the
Bio/SimpleAlign::slice

BUT my problem being that I want some module that will decide what
regions to cut dpending on the secondary structure features of the
sequences.

In other words.. I want a program to be able to judge the secondary str
of all the sequences in the multiple sequence alignment and extract the
region where all sequences have a consensus of the sec str.

All sequences in the alignment have known pdb structures, so the
secondary str information could be available in multiple formats- like
from pdb file itself or dssp output file etc. 

I have gone through the FAQS and HOWTO's at Bioperl but could not come
up with anything suitable.
If anyone can please guide me to any such existing modules that even
approximate the task.. I should probably be able to put it together to
fit the bill or at least know where to get started.

Thanks,
-Manisha