DARN! is a software tool for ncRNA localization. The problem of finding new occurrences of characterized ncRNAs can be modeled as the problem of finding all locally-optimal solutions of a weighted constraint network using dedicated weighted global constraints, encapsulating pattern-matching algorithms and data structures.
Darn! is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).
Darn! uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM, snoRNA C/D-box and tRNA search.
The predictions could be available in GFF, FASTA and other formats (see section 4).
Darn! can be use on line at this address: http://carlit.toulouse.inra.fr/Darn.
Darn! was developped by Matthias Zytnicki during his PhD in the BIA lab at INRA Toulouse, Franc