[BiO BB] protein secondary structure alignment

Raj rajkumar.bondugula at gmail.com
Thu Oct 5 15:50:57 EDT 2006

Hello all,
            Does any one know a nice tool to perfom secondary struture
alignment (similar to BLAST multiple sequence alignment on protein
sequences). The query to the program is secondary structure sequence.
The database contains a bunch of secondary structure sequences
(secondary structures corresponding to the proteins in my local
         The reason is I want to retrive structural homolog when the
sequence identity between the query protein is too low with any of the
proteins in the database.  I am aware of SSEA. It is a wonderful
program, except that I could not get it to compile that program on
Windows (both cygwin and VC++), inspite of spending weeks of time.
         Ideally, it would be great if I could modify NCBI BLAST (I
know I am being greedy, but PSIBLAST) to search for structural
homologies (input is a secondary structure sequence, the BLAST
databases made up of secondary structures and modify the appropriate
scoring matrices). Did any one try this?


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