Download:
[PostScript]
[PDF]
[Supplemental Material]
Titel:
Alignment of RNA Base Pairing Probability Matrices
Author(s):
Ivo L. Hofacker
Stephan H.F. Bernhart
Peter F. Stadler
To appear in:
Bioinformatics 2004;
Abstract:
Motivation
Many classes of functional RNA molecules are characterized by highly
conserved secondary structures but little detectable sequence similarity.
Reliable multiple alignments can therefore be constructed only when the
shared structural features are taken into account. Since multiple
alignments are used as input for many subsequent methods of data analysis,
structure based alignments are an indispensable necessity in RNA
bioinformatics.
Results
We present here a method to compute pairwise and progressive multiple
alignments from the direct comparison of basepairing probability matrices.
Instead of attempting to solve the folding and the alignment problem
simultaneously as in the classical Sankoff algorithm we use McCaskill's
approach to compute base pairing probability matrices which effectively
incorporate the information on the energetics of each sequences. A novel,
simplified variant of Sankoff's algorithms can then be employed to extract
the maximum weight common secondary structure and an associated alignment.
Availability
The programs pmcomp and pmmulti described in this
contribution are implemented in Perl, and are available on
request from the authors. A web server is available at
http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl
Keywords:
Sankoff Algorithm, RNA Secondary Structure, Structure-Based Alignments
Return to 2003 working papers list.
Last modified: 2004-05-05 14:29:27 ivo