{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:06:50Z","timestamp":1780110410126,"version":"3.54.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.<\/jats:p>\n               <jats:p>Availability: RNAshapes is freely available at as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package.<\/jats:p>\n               <jats:p>Contact: \u00a0psteffen@techfak.uni-bielefeld.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btk010","type":"journal-article","created":{"date-parts":[[2005,12,16]],"date-time":"2005-12-16T01:24:29Z","timestamp":1134696269000},"page":"500-503","source":"Crossref","is-referenced-by-count":246,"title":["RNAshapes: an integrated RNA analysis package based on abstract shapes"],"prefix":"10.1093","volume":"22","author":[{"given":"Peter","family":"Steffen","sequence":"first","affiliation":[{"name":"Faculty of Technology and, Bielefeld University 1 \u00a0 1 \u00a0 \u00a0 33594 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"Vo\u00df","sequence":"additional","affiliation":[{"name":"Institute of Biology II, Experimental Bioinformatics, Freiburg University 3 \u00a0 3 \u00a0 \u00a0 Sch\u00e4nzlestr. 1, 79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Rehmsmeier","sequence":"additional","affiliation":[{"name":"Center for Biotechnology (Ce BiTec), Bielefeld University 2 \u00a0 2 \u00a0 \u00a0 33594 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Reeder","sequence":"additional","affiliation":[{"name":"Faculty of Technology and, Bielefeld University 1 \u00a0 1 \u00a0 \u00a0 33594 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Giegerich","sequence":"additional","affiliation":[{"name":"Faculty of Technology and, Bielefeld University 1 \u00a0 1 \u00a0 \u00a0 33594 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2005,12,15]]},"reference":[{"key":"2023012408514065200_b1","doi-asserted-by":"crossref","first-page":"7280","DOI":"10.1093\/nar\/gkg938","article-title":"A statistical sampling algorithm for RNA secondary structure prediction","volume":"31","author":"Ding","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012408514065200_b2","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/1471-2105-5-140","article-title":"A comprehensive comparison of comparative RNA structure prediction","volume":"5","author":"Gardner","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012408514065200_b3","doi-asserted-by":"crossref","first-page":"4843","DOI":"10.1093\/nar\/gkh779","article-title":"Abstract shapes of RNA","volume":"32","author":"Giegerich","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012408514065200_b4","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1093\/bioinformatics\/bti279","article-title":"Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%","volume":"21","author":"Havgaard","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408514065200_b5","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatshefte f. Chemie"},{"key":"2023012408514065200_b6","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1006\/jmbi.2001.5351","article-title":"Dynalign: an algorithm for finding the secondary structure common to two RNA sequences","volume":"317","author":"Mathews","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023012408514065200_b7","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"2023012408514065200_b8","doi-asserted-by":"crossref","first-page":"3516","DOI":"10.1093\/bioinformatics\/bti577","article-title":"Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction","volume":"21","author":"Reeder","year":"2005","journal-title":"Bioinformatics"},{"issue":"5","key":"2023012408514065200_b9","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1137\/0145048","article-title":"Simultaneous solution of the RNA folding, alignment and protosequence problems","volume":"45","author":"Sankoff","year":"1985","journal-title":"SIAM J. Appl. Math."},{"key":"2023012408514065200_b10","first-page":"387","article-title":"An algorithm for comparing multiple RNA secondary structures","volume":"4","author":"Shapiro","year":"1988","journal-title":"Comput. Appl. Biosci."},{"key":"2023012408514065200_b11","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G","article-title":"Complete suboptimal folding of RNA and the stability of secondary structures","volume":"49","author":"Wuchty","year":"1999","journal-title":"Biopolymers"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/4\/500\/48840486\/bioinformatics_22_4_500.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/4\/500\/48840486\/bioinformatics_22_4_500.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:24:01Z","timestamp":1674552241000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/4\/500\/184565"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,12,15]]},"references-count":11,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2006,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btk010","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,2,15]]},"published":{"date-parts":[[2005,12,15]]}}}