RNAsalsa
Structured RNAs and the Accurate and Efficient Reconstruction of Deep Phylogenies
The software package RNAsalsa serves as a framework to
perform improved RNA structure predictions as well as alignments of
structural RNA sequences. It utilizes prior knowledge about structural
patterns, adapted constraint directed thermodynamic folding
algorithms, and comparative evidence methods. It automatically and
simultaneously generates both highly corrected individual secondary
structure predictions within a set of homologous RNA genes and a
consensus structure for the set, and it takes then sequence and
structure information into account as part of the alignment's scoring
function. RNAsalsa uses structure information for adjusting
and refining the sequence alignment and vice versa.
Phylogeny reconstruction tasks are the main group of applications for RNAsalsa; methods can be extended to RNA secondary structure,
incorporating both the RNAsalsa derived (and mostly improved)
models for the secondary structure elements of the RNA and also the
alignment based on that extended structure information. Thus, it is
possible to make the slower evolution of the structural features a
reproducible source of information.
The current version of RNAsalsa is command line based and
available either as source code, or as a pre-compiled executable for
various common operating systems.
Current version:
RNAsalsa 0.8.1
[Download of source codes as .tar.gz
archive]
[Download of source codes as ZIP
file]
[Download of MS Windows (32bit) executable as ZIP file]
[The manual]
If you find this software useful for your research, please cite the
following work:
- Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Roman R. Stocsits, Harald Letsch, Jana Hertel, Bernhard Misof, and Peter F. Stadler
Nucleic Acids Res. 2009 Sep 1. [Epup ahead of print], doi:10.1093/nar/gkp600
<rnasalsa@gmail.com>
Last modified: 2009-10-13 09:50:00 roman