Homology search with fragmented nucleic acid sequence patterns

Axel Mosig, Julian Chen, Peter F. Stadler

Research output: Chapter in Book/Report/Conference proceedingConference contribution

20 Scopus citations


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 be deleted, i.e., have no match in the current region of the genome. The program furthermore estimates p- and E-values for the matches. We apply fragrep2 to homology searches for RNase MRP, unveiling two previously unidentified matches as well as reproducing the results of two previous surveys. Furthermore, we complement the picture of vertebrate vault RNAs, a class of ncRNAs that has not received much attention so far.

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
PublisherSpringer Verlag
Number of pages11
ISBN (Print)9783540741251
StatePublished - 2007
Event7th International Workshop on Algorithms in Bioinformatics, WABI 2007 - PhiIadelphia, PA, United States
Duration: Sep 8 2007Sep 9 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4645 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Country/TerritoryUnited States
CityPhiIadelphia, PA

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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