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

doi:10.1093/bioinformatics/btm439

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

Chemistry

Research output: Contribution to journal › Article › peer-review

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 language	English (US)
Pages (from-to)	2959-2960
Number of pages	2
Journal	Bioinformatics
Volume	23
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btm439
State	Published - Nov 2007

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btm439

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title = "RagPools: RNA-As-Graph-Pools-a web server for assisting the design of structured RNA pools for in vitro selection",

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.",

author = "Namhee Kim and Shin, {Jin Sup} and Shereef Elmetwaly and Gan, {Hin Hark} and Tamar Schlick",

note = "Funding Information: This work was supported by Human Frontier Science Program (HFSP) and by a joint NSF/NIGMS Initiative in Mathematical Biology (DMS-0201160).",

year = "2007",

month = nov,

doi = "10.1093/bioinformatics/btm439",

language = "English (US)",

volume = "23",

pages = "2959--2960",

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AU - Elmetwaly, Shereef

AU - Gan, Hin Hark

AU - Schlick, Tamar

N1 - Funding Information: This work was supported by Human Frontier Science Program (HFSP) and by a joint NSF/NIGMS Initiative in Mathematical Biology (DMS-0201160).

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N2 - 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.

AB - 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.

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

Abstract

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