Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 04-019

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Titel:
fragrep: Efficient Search for Fragmented Patterns in Genomic Sequences

Author(s):
Axel Mosig, Katrin Sameith, Peter F. Stadler

Submitted for publication
Abstract:
Many classes of non-coding RNAs (including yRNAs, vaultRNAs, RNAse P and MRP RNA, 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 length. Local alignment algorithms such as blast are therefore ill-suited for the discovery new homologs of such ncRNAs in genomic sequences. The fragrep tool instead implements an efficient algorithm for detecting pattern fragments that occur in a given order. For each pattern fragment a mismatches tolerance and bounds on the length of the intervening sequences can be specified separately.


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