(Parallel) RNA Alignment by Genetic
RAGA: RNA alignment by Genetic Algorithm, C.Notredame,
E.A. O'Brien, D.G. Higgins, Nucleic Acid Research, Vol. 25, 4570-4580,
WHAT IS RAGA?
available in [ps][pdf][html].
RAGA is a pairwise alignment program. Its aim is to align two RNA sequences,
sharing the same secondary structure but different primary sequences, knowing
the secondary structure of one of the RNAs. We tested RAGA on a range of
testcases made from Ribosomal RNA sequences extracted from the Ribosomal
Small Subunit Database. Our result clearly suggest that RAGA is able
to take into account secondary structure information, in order to generate
accurate alignments. We also found that RAGA was able to deal with some
tertiary elements like pseudoknots.
WHAT IS PRAGA?
RAGA is mostly an adaptation of SAGA. It
can align two sequence up to 2000 nucleotide long. The way it is now, PRAGA
can only align a pair of sequences, but in a short term we plan to have
one of these two sequences replaced by a profile made from some reference
PRAGA is a parallel GA, designed to speed up RAGA. In fact it is a
module, that can start several processes of RAGA in parallel and control
them. While these GAs run, PRAGA monitors them, and allows them to exchange
part of their population. In the worst case, PRAGA is as fast as a single
RAGA process with an overall population of the same size as the total population
of the RAGA processes in the parallell version. In the best case, the speedup
is much higher and the accuracy significantly improved, due to the way
the Processes are exchanging population.
WHAT IS IN THE PACKAGE ?
DOWNLOADING RAGA and PRAGA
The module itself PGA is compatible with SAGA
and will be supported to remain compatible with RAGA and any new GA based
on SAGA, that we may develop in the future.
RAGA and PRAGA can be obtained
throught this page. To download the packages, click HERE.
is included in the package itself. To install the programs, use the README
and the documentation. Install RAGA first, and then PRAGA if you need it.
Please be aware that installing PRAGA is more difficult than RAGA. If
you have any problem following the procedures indicated in the Documentation,
please refer first to your system manager.