Strategies for Homology-Based ncRNA Gene Annotation

Most non-coding RNAs are short and /or poorly conserved in sequence. Most of the longer examples , furthermore, consist of a collection of conserved structural motifs rath er at a coherent globally conserved secondary structure. As a consequence, the conceptually simple problem of homology search becomes a complex and technically demanding task. Despite the best e fforts of databases such as Rfam, the situation is complicated further by the sparsity of inf ormation on many — in particular prokaryotic — RNA families. In th is contribution we review recent e fforts to customize sequence-based search tools for ncRNA applications. In par ticul r semi-global alignments and the development of methods for fragmented pattern search have brought signific a t practical advances. Current developments in this area focus on the integration of fragmented sequence patter n search with search algorithms for secondary structure patterns. As one example, we introduce here fragrep3.

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