> In article <1994Jan13.191610.15552 at alw.nih.gov> bergsage at helix.nih.gov (Peter Leif Bergsagel) writes:
> >I have the sequence of different stretches of RNA that bind to a protein. I
> >am trying to develop a consensus RNA binding site. I suspect that it is
> >related to the secondary (or tertiary) structure. When I plot these out
> >using FOLD I have a very hard time comparing one structure to another, yet
> >alone a whole series. Are there any suggestions for how to determine the
> >consensus site sequence ?
There is a tree analysis program called Newtree that compares the output
region files from Zukers mfold program. It is available by anonymous ftp
from nrcbsa.bio.nrc.ca in the directory /pub. It is written in pascal, the
iris version is supplied, the vax version is obtained by decommenting the
file handling routines (open, reset rather than rewrite etc.). You could
run it on a micro if you fiddle a little. This program produces a region
file containing the conserved structures. I am just starting to use this
program to analyze the output of overlapping folds on a 17kb rna from two
species...not the sort of thing you want to do by eye. :)
Regards,
Matthew
