In article <kramer.1120160442A at 129.49.21.115> kramer at mcbsgi.bio.sunysb.edu (Joe Kramer) writes:
>I was wondering what the best way to deal with 35-40 25 nucleotide
>sequences obtained during the course of a selex procedure would be. I am
>interested in developing a consensus sequence. Anything that I could use
>at my mac would be preferred.
Joe,
Detecting an RNA consensus sequence and structure in a family of SELEX
babies is an open research problem. So far as I know, the best current
solution is to do it by eye, guided by the output from an RNA folding
program (such as Zuker's MFOLD, available at many ftp sites; probably
at Don Gilbert's site for Macs) and possibly from a program that looks
for primary sequence consensus alone (check out WCONSENSUS, from Hertz
and Stormo, available by anonymous ftp from beagle.colorado.edu, but
probably no Mac version).
I've been developing algorithms that deal with RNA consensus secondary
and primary structure simultaneously so I can find a consensus in a
family of small RNAs, and SELEX babies are exactly what I have in
mind. Though the core of this work is complete (Eddy & Durbin, NAR, in
press this week) there are a number of rough edges yet (the main one
having to do with finding a small consensus buried in a longer
sequence) and the programs, though fairly clean and distributable, do
not have nice front ends for users. Also, I've only ever ported the
code to different UNIX platforms, never a Mac. However, that said,
the source code is available by anonymous ftp from
cele.mrc-lmb.cam.ac.uk, as pub/sre/cove-2.2.tar.Z, and the preprint of
the NAR paper is there as cove-inpress-NAR.ps.Z. It might be useful
to you, and it'd probably spur further development from me if people
had a go at SELEX babies with my code.
--
- Sean Eddy
- MRC Laboratory of Molecular Biology, Cambridge, England
- sre at mrc-lmb.cam.ac.uk
