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{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,19]],"date-time":"2023-09-19T13:24:06Z","timestamp":1695129846956},"reference-count":38,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2023,8]]},"abstract":"<jats:p> Most of the functional RNA elements located within large transcripts are local. Local folding therefore serves a practically useful approximation to global structure prediction. Due to the sensitivity of RNA secondary structure prediction to the exact definition of sequence ends, accuracy can be increased by averaging local structure predictions over multiple, overlapping sequence windows. These averages can be computed efficiently by dynamic programming. Here we revisit the local folding problem, present a concise mathematical formalization that generalizes previous approaches and show that correct Boltzmann samples can be obtained by local stochastic backtracing in McCaskill\u2019s algorithms but not from local folding recursions. Corresponding new features are implemented in the ViennaRNA package to improve the support of local folding. Applications include the computation of maximum expected accuracy structures from RNAplfold data and a mutual information measure to quantify the sensitivity of individual sequence positions. <\/jats:p>","DOI":"10.1142\/s0219720023500166","type":"journal-article","created":{"date-parts":[[2023,6,8]],"date-time":"2023-06-08T14:27:51Z","timestamp":1686234471000},"source":"Crossref","is-referenced-by-count":0,"title":["Local RNA folding revisited"],"prefix":"10.1142","volume":"21","author":[{"given":"Maria","family":"Waldl","sequence":"first","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Wien, Austria"}]},{"given":"Thomas","family":"Spicher","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Wien, Austria"}]},{"given":"Ronny","family":"Lorenz","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Wien, Austria"}]},{"given":"Irene K.","family":"Beckmann","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Wien, Austria"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Wien, Austria"}]},{"given":"Sarah Von","family":"L\u00f6hneysen","sequence":"additional","affiliation":[{"name":"Institute of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig, Germany"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Institute of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig, Germany"}]}],"member":"219","published-online":{"date-parts":[[2023,7,28]]},"reference":[{"key":"S0219720023500166BIB001","doi-asserted-by":"crossref","first-page":"6631","DOI":"10.1128\/JVI.79.11.6631-6643.2005","volume":"79","author":"Alvarez DE","year":"2005","journal-title":"J Virol"},{"key":"S0219720023500166BIB003","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btk014","volume":"22","author":"Bernhart S","year":"2006","journal-title":"Bioinformatics"},{"key":"S0219720023500166BIB004","first-page":"3","volume":"6","author":"Bernhart SH","year":"2011","journal-title":"Alg Mol Biol"},{"key":"S0219720023500166BIB005","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1007\/s00285-011-0467-8","volume":"65","author":"Clote P","year":"2012","journal-title":"J Math Biol"},{"key":"S0219720023500166BIB
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