Searching for 2D RNA geometries in bacterial genomes

Uri Laserson, Hin Hark Gan, Tamar Schlick

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

Abstract

A method to search for specific RNA geometries in the genomes of bacterial organisms, is discussed. The method is comprised of three steps such as motif descriptor construction, genome search and analysis of candidate sequence. After initially filtering the pool of candidates by predicting whether they adopt the correct geometry, the remaining candidates are subjected to two energetic analysis to evaluate their stability, an analysis of heat capacity curves and the generation of conformational energy landscape. The search methodology is expected to be applied in vitro selection technology as a tool for identifying novel RNA genes or RNA-based regulatory mechanisms.

Original languageEnglish (US)
Title of host publicationProceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04)
Pages373-377
Number of pages5
StatePublished - 2004
EventProceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04) - Brooklyn, NY, United States
Duration: Jun 9 2004Jun 11 2004

Other

OtherProceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04)
CountryUnited States
CityBrooklyn, NY
Period6/9/046/11/04

Fingerprint

RNA
Genome
Genes
Geometry
Energy Landscape
Heat Capacity
Descriptors
Specific heat
Filtering
Gene
Curve
Methodology
Evaluate

ASJC Scopus subject areas

  • Software
  • Geometry and Topology
  • Safety, Risk, Reliability and Quality
  • Chemical Health and Safety

Cite this

Laserson, U., Gan, H. H., & Schlick, T. (2004). Searching for 2D RNA geometries in bacterial genomes. In Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04) (pp. 373-377)

Searching for 2D RNA geometries in bacterial genomes. / Laserson, Uri; Gan, Hin Hark; Schlick, Tamar.

Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04). 2004. p. 373-377.

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

Laserson, U, Gan, HH & Schlick, T 2004, Searching for 2D RNA geometries in bacterial genomes. in Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04). pp. 373-377, Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04), Brooklyn, NY, United States, 6/9/04.
Laserson U, Gan HH, Schlick T. Searching for 2D RNA geometries in bacterial genomes. In Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04). 2004. p. 373-377
Laserson, Uri ; Gan, Hin Hark ; Schlick, Tamar. / Searching for 2D RNA geometries in bacterial genomes. Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04). 2004. pp. 373-377
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