Consan - pairwise stochastic context-free grammar for RNA structural alignment Version 1.1 (September 2006) Copyright (C) 2006 HHMI/Washington University School of Medicine -------------------------------------------------------------------- o About this software... Consan is an implementation of a pairwise stochastic context-free grammar for RNA structural alignment, both unconstrained and constrained on alignment pins. o Getting Consan WWW home: http://selab.genetics.wustl.edu/people/robin/consan/ o Installing Consan See the file INSTALL for brief instructions. You should also read the following files: LICENSE -- Full text of the GNU Public License, version 2 o Getting started with Consan There are three executables: strain_ml, sfold, and scompare. Brief descriptions and basic usage: * strain_ml (training; generates a model parameter file e.g. model.mod) > strain_ml -s model.mod trainingset.stk * sfold (structural alignment of two sequences) > sfold -m model.mod seq1.fa seq2.fa * scompare (structural alignment of two sequences with comparison to a given pairwise alignment; essentially a wrapper around sfold) > scompare -m model.mod alignment.stk Run any of the above programs with the -h options for more options. See the file paperguide.txt for examples of how the software was used in the paper (see reference below). o References for Consan Dowell, R.D. and S.R. Eddy "Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints" BMC Bioinformatics 7:41 2006. o Reporting bugs These programs are under active development. Though this release has been tested and appears to be stable, bugs may crop up. If you use these programs, please help me out and e-mail me with suggestions, comments, and bug reports. (rdd@mit.edu) Robin Dowell & Sean Eddy Howard Hughes Medical Institute and Dept. of Genetics Washington University School of Medicine, St. Louis, Missouri, USA -------------------------------------------------------------------