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Nucleic Acids Res. 2012 Jul;40(Web Server issue):W29-34. doi: 10.1093/nar/gks412. Epub 2012 May 16.

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

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1
Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. ykato@is.naist.jp

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/.

PMID:
22600734
PMCID:
PMC3394313
DOI:
10.1093/nar/gks412
[Indexed for MEDLINE]
Free PMC Article
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