Inexact graph matching by "geodesic hashing" for the alignment of pseudoknoted RNA secondary structures

Mira Abraham, Haim J. Wolfson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Non-coding RNAs are transcripts that do not encode proteins play key roles in many biological processes. The alignment of their secondary structures has become a major tool in RNA functional annotation. Many of the non-coding RNAs contain pseudoknots as a structural motif, which proved to be functionally important. We present HARP, a heuristic algorithm for the pairwise alignment of non-restricted (arbitrary) classes of pseudoknotted RNA secondary structures. HARP applies "geodesic hashing" to perform inexact matching of specially defined reduced RNA secondary structure graphs. The method proved to be efficient both in time and memory and was successfully tested on a benchmark of available experimental structures with known function. A web server is available at http://bioinfo3d.cs.tau.ac.il/HARP/.

Original languageEnglish
Title of host publicationProceedings of the Prague Stringology Conference 2011
Pages45-58
Number of pages14
StatePublished - 2011
EventPrague Stringology Conference 2011, PSC 2011 - Prague, Czech Republic
Duration: 29 Aug 201131 Aug 2011

Publication series

NameProceedings of the Prague Stringology Conference 2011

Conference

ConferencePrague Stringology Conference 2011, PSC 2011
Country/TerritoryCzech Republic
CityPrague
Period29/08/1131/08/11

Keywords

  • Geodesic distances
  • Geometric hashing
  • Inexact graph matching
  • Non-coding RNA
  • RNA structure alignment
  • Secondary structure with pseudoknots

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