(P)RAGA HOME PAGE
(Parallel) RNA Alignment by Genetic Algorithm

RAGA: RNA alignment by Genetic Algorithm, C.Notredame, E.A. O'Brien, D.G. Higgins, Nucleic Acid Research, Vol. 25, 4570-4580, 1997.
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.

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 alignment.

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.

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.

-A list of the testcases we used to test PRAGA

-The code for RAGA and some documentation.

-The code for PRAGA and some documentation.

RAGA and PRAGA can be obtained throught this page. To download the packages, click HERE. The Documentation 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.