{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:10:19Z","timestamp":1760955019258},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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 \u2018mixing matrix\u2019 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 (\u2018Designer\u2019 component) provides optimized starting sequences, mixing matrices and associated weights in response to a user-specified target pool structure distribution. In addition, RagPools (\u2018Analyzer\u2019 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.<\/jats:p><jats:p>Availability: The web server is accessible on the web at http:\/\/rubin2.biomath.nyu.edu<\/jats:p><jats:p>Contact: \u00a0schlick@nyu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm439","type":"journal-article","created":{"date-parts":[[2007,9,14]],"date-time":"2007-09-14T00:23:31Z","timestamp":1189729411000},"page":"2959-2960","source":"Crossref","is-referenced-by-count":24,"title":["R<scp>ag<\/scp>P<scp>ools<\/scp>: RNA-As-Graph-Pools\u2014a web server for assisting the design of structured RNA pools for<i>in vitro<\/i>selection"],"prefix":"10.1093","volume":"23","author":[{"given":"Namhee","family":"Kim","sequence":"first","affiliation":[{"name":"1 Department 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"}]},{"given":"Jin Sup","family":"Shin","sequence":"additional","affiliation":[{"name":"1 Department 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"}]},{"given":"Shereef","family":"Elmetwaly","sequence":"additional","affiliation":[{"name":"1 Department 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"}]},{"given":"Hin Hark","family":"Gan","sequence":"additional","affiliation":[{"name":"1 Department 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"}]},{"given":"Tamar","family":"Schlick","sequence":"additional","affiliation":[{"name":"1 Department 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"},{"name":"1 Department 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"}]}],"member":"286","published-online":{"date-parts":[[2007,9,13]]},"reference":[{"key":"2023041107264110900_","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1261\/rna.7271405","article-title":"In vitro RNA random pools are not structurally diverse: a computational analysis","volume":"11","author":"Gevertz","year":"2005","journal-title":"RNA"},{"key":"2023041107264110900_","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1261\/rna.374907","article-title":"A computational proposal for designing structured RNA pools for in vitro selection of RNAs","volume":"13","author":"Kim","year":"2007","journal-title":"RNA"},{"key":"2023041107264110900_","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1146\/annurev.biochem.68.1.611","article-title":"In vitro selection of functional nucleic acids","volume":"68","author":"Wilson","year":"1999","journal-title":"Annu. Rev. Biochem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2959\/49821202\/bioinformatics_23_21_2959.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2959\/49821202\/bioinformatics_23_21_2959.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T04:11:39Z","timestamp":1684037499000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/21\/2959\/372753"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,13]]},"references-count":3,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2007,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm439","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,11,1]]},"published":{"date-parts":[[2007,9,13]]}}}