RagPools

RNA-As-Graph-Pools-a web server for assisting the design of structured RNA pools for in vitro selection

Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

Summary: Our RNA-As-Graph-Pools (RagPools web server offers a theoretical companion tool for RNA in vitro selection and related problems. Specifically, it suggests how to construct RNA sequence/structure pools with user-specified properties and assists in analyzing resulting distributions. This utility follows our recently developed approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a 'mixing matrix' approach combined with a graph theory analysis of RNA secondary-structure space; the mixing matrix specifies nucleotide transition rates, and graph theory links sequences to simple graphical objects representing RNA motifs. The companion RagPools web server ('Designer' component) provides optimized starting sequences, mixing matrices and associated weights in response to a user-specified target pool structure distribution. In addition, RagPools ('Analyzer' component) analyzes the motif distribution of pools generated from user-specified starting sequences and mixing matrices. Thus, RagPools serves as a guide to researchers who aim to synthesize RNA pools with desired properties and/or experiment in silico with various designs by our approach.

Original languageEnglish (US)
Pages (from-to)2959-2960
Number of pages2
JournalBioinformatics
Volume23
Issue number21
DOIs
StatePublished - Nov 2007

Fingerprint

Web Server
RNA
Servers
Graph in graph theory
Graph theory
Mixing Sequence
RNA Secondary Structure
Nucleotide Motifs
Sequence Space
Computer Simulation
Nucleotides
Research Personnel
Engineering
Weights and Measures
Target
Design
In Vitro Techniques
Experiment

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

RagPools : RNA-As-Graph-Pools-a web server for assisting the design of structured RNA pools for in vitro selection. / Kim, Namhee; Shin, Jin Sup; Elmetwaly, Shereef; Gan, Hin Hark; Schlick, Tamar.

In: Bioinformatics, Vol. 23, No. 21, 11.2007, p. 2959-2960.

Research output: Contribution to journalArticle

Kim, Namhee ; Shin, Jin Sup ; Elmetwaly, Shereef ; Gan, Hin Hark ; Schlick, Tamar. / RagPools : RNA-As-Graph-Pools-a web server for assisting the design of structured RNA pools for in vitro selection. In: Bioinformatics. 2007 ; Vol. 23, No. 21. pp. 2959-2960.
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