Is there existing software to display the predicted secondary structure
of aligned sequences? I think this would be very useful, and I am going to
write something if nothing already exists. I would like a program that could
combine the output of PILEUP and PEPTIDESTRUCTURE to produce a table like the
one below. If any one knows of any such software, or has any suggestions of
other considerations I should take in writing such a program, then I would
appreciate the information. If I do end up writing such a program, I will
gladly give a copy to anyone who wants one.
Sample Output (This is more or less bogus data meant only to show how the
output could be formatted. I use the Chou-Fasman prediction below, however,
a second similar set of output using the Garnier-Osguthorpe-Robson method
would also be generated.)
Sequence 1 KTFGELKNLPLLNT
Sequence 2 SVADQK..FLNVAK
and so on to
Sequence n SEW...QIGQPFVA
Skip Cole rcole at ncsa.uiuc.edu
ps. I am using e-mail to post this, so please mail all responses back to me.
If there is significant interest, then I will summarize this and make
another posting. Thank you.