Searching RNA motifs and their intermolecular contacts with constraint networks.
BACKGROUND
Searching RNA gene occurrences in genomic sequences is a task whose importance has been renewed by the recent discovery of numerous functional RNA, often interacting with other ligands. Even if several programs exist for RNA motif search, none exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules.


RESULTS
We present a constraint network formulation of this problem. RNA are represented as structured motifs that can occur on more than one sequence and which are related together by possible hybridization. The implemented tool MilPat is used to search for several sRNA families in genomic sequences. Results show that MilPat allows to efficiently search for interacting motifs in large genomic sequences and offers a simple and extensible framework to solve such problems. New and known sRNA are identified as H/ACA candidates in Methanocaldococcus jannaschii.


BACKGROUND
http://carlit.toulouse.inra.fr/MilPaT/MilPat.pl.
Thébault
P
P
Unité de Biométrie & Intelligence Artificielle, INRA, Chemin de Borde Rouge Auzeville, BP 52627, 31326 Castanet-Tolosan, France.
de Givry
S
S
Schiex
T
T
Gaspin
C
C
D000465:Algorithms; D020816:Amino Acid Motifs; D001185:Artificial Intelligence; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D011485:Protein Binding; D012313:RNA / Q000235:genetics* / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*
D016601:RNA-Binding Proteins; D012313:RNA