Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming

Yuki Kato; Kengo Sato; Kiyoshi Asai; Tatsuya Akutsu

doi:10.1093/nar/gks412

Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming

Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu

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

14 Citations (Scopus)

Abstract

We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.

Original language	English
Pages (from-to)	W29-W34
Journal	Nucleic acids research
Volume	40
Issue number	W1
DOIs	https://doi.org/10.1093/nar/gks412
Publication status	Published - 2012 Jul
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gks412

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title = "Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming",

abstract = "We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.",

author = "Yuki Kato and Kengo Sato and Kiyoshi Asai and Tatsuya Akutsu",

note = "Funding Information: Grant-in-Aid for Young Scientists (B) from Japan Society for the Promotion of Science [#22700313 to Y.K., #22700305 to K.S.]. Funding for open access charge: Grant-in-Aid for Challenging Exploratory Research from Japan Society for the Promotion of Science [#23650153].",

year = "2012",

month = jul,

doi = "10.1093/nar/gks412",

language = "English",

volume = "40",

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T2 - Fast and accurate tools for RNA 2D structure prediction using integer programming

AU - Kato, Yuki

AU - Sato, Kengo

AU - Asai, Kiyoshi

AU - Akutsu, Tatsuya

N1 - Funding Information: Grant-in-Aid for Young Scientists (B) from Japan Society for the Promotion of Science [#22700313 to Y.K., #22700305 to K.S.]. Funding for open access charge: Grant-in-Aid for Challenging Exploratory Research from Japan Society for the Promotion of Science [#23650153].

PY - 2012/7

Y1 - 2012/7

N2 - We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.

AB - We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.

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Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming

Abstract

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