ABCC : Application's document Page

RNAGA

RNA Analysis, Sequence Analysis, Bioinformatics

Shuyun Le, Bob Stephens and Jigui Shan
Advanced Biomedical Computing Center(ABCC)

A program for predicting a secondary structure common to a number of phylogenetically related 
sequences without the need for pre-aligned RNA sequences. One of the remarkable features of 
RNAGA is that RNA secondary structures are automatically optimized by not only the free energy 
of the formation of the structure but also the structural similarity among homologous sequences. 
The program operates in three stages. In the first stage, a genetic algorithm (GA) is used to 
generate a population of RNA secondary structures that satisfy certain conditions of 
thermodynamic stability. In this step, the free energy of a folded structure is taken as a 
fitness criterion. Secondly, we define a measure of structural conservation for the structure 
from one sequence with respect to those in other sequences. With this conservation measure as 
the fitness criterion, GA is then used to improve the structural similarity among homologous 
RNAs for the structures in the population of a sequence. Finally, those structures that satisfy 
certain conditions of thermodynamic stability and structural conservation are selected as 
predicted common structures for a set of homologous RNAs. These predictions are ranked in 
descending order based on the structural conservation score. The program is based on the genetic 
algorithm and implemented in Fortran 90 running on Unix.

IRIX64

/abcc/apps/`uname`/lecb/rnaga 

for web use:
http://www.abcc.ncifcrf.gov/app/htdocs/appdb/drawpage.php?appname=RNAGA 
for commandline use:
./rnaga

http://protein3d.ncifcrf.gov/shuyun/rnaga.html

Bob Stephens
(301)846-5787
bobs@ncifcrf.gov

Jigui Shan
(301)846-5157
shanj@ncifcrf.gov

Jigui Shan and Bob Stephens