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Bioinformatics Advance Access originally published online on September 13, 2007
Bioinformatics 2007 23(21):2959-2960; doi:10.1093/bioinformatics/btm439
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Namhee Kim 1, Jin Sup Shin 1, Shereef Elmetwaly 1, Hin Hark Gan 1 and Tamar Schlick 1,2,*

1Department of Chemistry, New York University, 100 Washington Square East, New York 10003 and 2Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York 10012, USA

*To whom correspondence should be addressed.


  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.

Availability: The web server is accessible on the web at http://rubin2.biomath.nyu.edu

Contact: schlick{at}nyu.edu

Associate Editor: Thomas Lengauer

Received on April 13, 2007; revised on August 6, 2007; accepted on August 20, 2007

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