{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T16:44:28Z","timestamp":1761324268521,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,23]],"date-time":"2020-01-23T00:00:00Z","timestamp":1579737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Joint Research Projects"},{"name":"Israeli Ministry of Science & Technology"},{"DOI":"10.13039\/100007225","name":"MOST","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012681","name":"CNRS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012681","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>RNA design has conceptually evolved from the inverse RNA folding problem. In the classical inverse RNA problem, the user inputs an RNA secondary structure and receives an output RNA sequence that folds into it. Although modern RNA design methods are based on the same principle, a finer control over the resulting sequences is sought. As an important example, a substantial number of non-coding RNA families show high preservation in specific regions, while being more flexible in others and this information should be utilized in the design. By using the additional information, RNA design tools can help solve problems of practical interest in the growing fields of synthetic biology and nanotechnology. incaRNAfbinv 2.0 utilizes a fragment-based approach, enabling a control of specific RNA secondary structure motifs. The new version allows significantly more control over the general RNA shape, and also allows to express specific restrictions over each motif separately, in addition to other advanced features.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>incaRNAfbinv 2.0 is available through a standalone package and a web-server at https:\/\/www.cs.bgu.ac.il\/incaRNAfbinv. Source code, command-line and GUI wrappers can be found at https:\/\/github.com\/matandro\/RNAsfbinv.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa039","type":"journal-article","created":{"date-parts":[[2020,1,16]],"date-time":"2020-01-16T13:50:12Z","timestamp":1579182612000},"page":"2920-2922","source":"Crossref","is-referenced-by-count":8,"title":["<tt>incaRNAfbinv 2.0<\/tt>: a webserver and software with motif control for fragment-based design of RNAs"],"prefix":"10.1093","volume":"36","author":[{"given":"Matan Drory","family":"Retwitzer","sequence":"first","affiliation":[{"name":"Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8481-1094","authenticated-orcid":false,"given":"Vladimir","family":"Reinharz","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, H2X 3Y7, Canada"},{"name":"Institute for Basic Science , Daejeon 34126, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Churkin","sequence":"additional","affiliation":[{"name":"Software Engineering Department , Sami Shamoon College of Engineering, Beer-Sheva 84100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Informatique de l\u2019\u00c9cole Polytechnique (LIX CNRS UMR 7161) , Ecole Polytechnique, Palaiseau 91120, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00e9r\u00f4me","family":"Waldisp\u00fchl","sequence":"additional","affiliation":[{"name":"School of Computer Science , McGill University Montr\u00e9al H3A 0E9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danny","family":"Barash","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,23]]},"reference":[{"key":"2023013111494906600_btaa039-B1","first-page":"350","article-title":"Design of RNAs: comparing programs for inverse RNA folding","volume":"19","author":"Churkin","year":"2018","journal-title":"Brief. 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