RNA secondary structure similarity identification

Matthew Wakefield genmjw at lure.latrobe.edu.au
Tue Jan 18 06:16:19 EST 1994

> 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.   :) 

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