Homology Search with Fragmented Nucleic Acid Sequence Patterns

The comprehensive annotation of non-coding RNAs in newly sequenced genomes is still a largely unsolved problem because many functional RNAs exhibit not only poorly conserved sequences but also large variability in structure. In many cases, such as Y RNAs, vault RNAs, or telomerase RNAs, sequences differ by large insertions or deletions and have only a few small sequence patterns in common. Here we present fragrep2, a purely sequence-based approach to detect such patterns in complete genomes. A fragrep2 pattern consists of an ordered list of position-specific weight matrices (PWMs) describing short, approximately conserved sequence elements, that are separated by intervals of non-conserved regions of bounded length. The program uses a fractional programming approach to align the PWMs to genomic DNA in order to allow for a bounded number of insertions and deletions in the patterns. These patterns are then combined to significant combinations of PWMs. At this step, a subset of PWMs may...

• Type: Conference
• Year: 2007
• Where: WABI
• Authors: Axel Mosig, Julian J.-L. Chen, Peter F. Stadler
• Keywords: Algorithms, Functional Rnas, Non-coding Rnas, RNAs, WABI 2007