Consan: pairwise structural RNA alignment

Description:

Pairwise RNA structural alignment, both unconstrained and constrained on alignment pins.

Source Code:

The Consan package contains source and minimal compile instructions. Consan was written in ANSI C and tested on Mandrake Linux.

consan-1.2.tar.gz

This is the Consan code only package (without datasets) as a single gzip'ed tar ball (692 KB).

consan-1.2_all.tar.gz

This is the complete Consan package (with datasets, described below) as a single gzip'ed tar ball (1.9 MB).

Version History

v1.0 Initial version.

v1.1 Improved documentation.

v1.2 Fixed bug which caused problems with long path names to dpswalign.

Documentation:

• README
• INSTALL
• LICENSE (GPL)
• paperguide.txt (Describes how Consan programs are used to generate the results reported in the paper referenced below).

Reference:

Dowell, RD and Eddy, SR. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 2006, 7:400.

Data Sets:

• notes.txt
• Training Set (mix80.stk)
• Rfam v7 Test Sets
  • Published Families excluding SSU (Rfam.v7.pub80.stk)
  • Random 100 5S and tRNA (R100.stk ; R100.pairs.stk)
  • Percent Identity Balanced Set (percid.stk)
• Dynalign Benchmarking Set (contact David H. Mathews)
• Stemloc Benchmarking Set (stemloc.stk)

Links to External Software:

• Dynalign
• Stemloc (part of Dart package)
• PMcomp
• Foldalign

Contributors and Acknowledgements

• Contributors of code include Robin Dowell, Sean Eddy, Robert J. Klein, and Elena Rivas.
• Testers include Shandy Wikman and Matt Yoder
• Acknowledgements to Sean Eddy, Ian Holmes, David Mathews, Ivo Hofacker, Jan Gorodkin, and Elena Rivas for intellectual contributions.