title: RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  The web server is accessible on the web at http://rubin2.biomath.nyu.edu
authors.affiliation: Department of Chemistry, New York University, 100 Washington Square East, New York 10003, USA.
authors.forename: Namhee
authors.initials: N
authors.lastname: Kim
authors.forename: Jin Sup
authors.initials: JS
authors.lastname: Shin
authors.forename: Shereef
authors.initials: S
authors.lastname: Elmetwaly
authors.forename: Hin Hark
authors.initials: HH
authors.lastname: Gan
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D020407:Internet; D008969:Molecular Sequence Data; D015347:RNA Probes / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D015347:RNA Probes