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Fragrep: an efficient search tool for fragmented patterns in genomic sequences.

Axel Mosig·Katrin Sameith·Peter Stadler
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Abstract

Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.

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AlgorithmsAnimalsBase Pair MismatchComputational BiologyDictyosteliumGenomeRNA, UntranslatedSequence Analysis, DNASoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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BibTeXRIS

Axel Mosig, Katrin Sameith, Peter Stadler. 2006. Fragrep: an efficient search tool for fragmented patterns in genomic sequences.. https://doi.org/10.1016/s1672-0229(06)60017-x

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