Title:
METHOD OF PREDICTING THE SECONDARY STRUCTURE OF RNA, PREDICTION APPARATUS AND PREDICTION PROGRAM
Document Type and Number:
WIPO Patent Application WO/2007/116787
Kind Code:
A1
Abstract:
It is intended to provide a method of predicting the secondary structure of an RNA
whereby the secondary structure of an RNA, the secondary structure of which has
been hardly predicted so far (for example, a pseudonot structure), can be predicted
and an apparatus for predicting the secondary structure of an RNA by using this
prediction method. The above method of predicting the secondary structure
of an RNA is characterized by comprising: the step of searching for bases capable
of constituting a stem structure in the subject RNA sequence; the step of setting
candidates for the stem structure based on the free energy of each of the bases
constituting the stem structure; the step of determining an identified stem
structure from among the stem structure candidates; the step of searching for
the sequential state of the RNA sequence based on the base data of the identified stem
structure as described above; the step of computing the sequential energy of
each of the bases constituting the RNA sequence based on the sequential structure state
as described above; and the step of setting an additional stem structure candidate
as a newly identified stem structure based on the sequential energy state of the
secondary structure of the RNA sequence, which reflects the identified stem
structure as described above, and the sequential energy state of the new secondary
structure in which the above secondary structure reflects an additional candidate
for the stem structure selected from among the above-described stem structure
candidates.
Inventors:
AKITOMI JOU (JP)
Application Number:
PCT/JP2007/056618
Publication Date:
October 18, 2007
Filing Date:
March 28, 2007
Export Citation:
Assignee:
NEC SOFTWARE LTD (JP)
AKITOMI JOU (JP)
AKITOMI JOU (JP)
International Classes:
G16B15/10; G06Q10/00; C12N15/09; G16B30/10
Foreign References:
| JPH08154677A | 1996-06-18 | |||
| JPH1074189A | 1998-03-17 | |||
| JP2003203077A | 2003-07-18 | |||
| JPH08154677A | 1996-06-18 |
Other References:
AKIYAMA Y.: "RNA no 2 Ji Kozo Yosoku", BIT, KYORITSU SHUPPAN, vol. 25, no. 10, 1 October 1993 (1993-10-01), pages 83 - 91, XP003018521
TANAKA T. ET AL.: "Kumiawase Saitekika Shuho ni yoru Pseudoknotted Structure Kozo o Fukunda RNA no Niji Kozo Yosoku (Prediction of RNA Secondary Structure Including Pseudoknotting Based on Combinational Optimization)", INFORMATION PROCESSING SOCIETY OF JAPAN KENKYU HOKOKU 96-MPS-10, vol. 96, no. 118, 26 November 1996 (1996-11-26), pages 25 - 32, XP003018522
YOSHIZAWA T. ET AL.: "RNA Niji Kozo Yosoku Shien System no Kaihatsu to Jisso (Developing RNA Secondary Structure Prediction Support System)", DAI 32 KAI REPORTS OF THE MEETING OF SPECIAL INTEREST GROUP ON FUNDAMENTAL THEORY OF ARTIFICIAL INTELLIGENCE (SIG-FAI-9703) THE JAPANESE SOCIETY FOR ARTIFICIAL INGELLIGENCE, 26 March 1998 (1998-03-26), XP003018523
GULTYAEV A.P.: "The computer simulation of RNA folding involving pseudoknot formation", NUCLEIC ACIDS RESEARCH, vol. 19, no. 9, 11 May 1991 (1991-05-11), pages 2489 - 2494, XP003018524
RUAN J. ET AL.: "An Iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots", BIOINFORMATICS, OXFORD UNIVERSITY ORESS, vol. 20, no. 1, 2004, pages 58 - 66, XP003018525
MINORU KANEHISA: "Invitation to post genome information", 10 June 2001, KYORITSU SHUPPAN CO. LTD., pages: 108 - 111
YASUSHI OKAZAKI; HIDEMASA BOUNOU: "Bioinformatics: Sequence and Genome Analysis", MEDICAL SCIENCES INTERNATIONAL LTD., pages: 212 - 242
GORODKIN ET AL.: "Discovering common stem-loop motifs in unaligned RNA sequences", NUCLEIC ACIDS RESEARCH, vol. 29, no. 10, 2001, pages 2135 - 2144
See also references of EP 2012246A4
TANAKA T. ET AL.: "Kumiawase Saitekika Shuho ni yoru Pseudoknotted Structure Kozo o Fukunda RNA no Niji Kozo Yosoku (Prediction of RNA Secondary Structure Including Pseudoknotting Based on Combinational Optimization)", INFORMATION PROCESSING SOCIETY OF JAPAN KENKYU HOKOKU 96-MPS-10, vol. 96, no. 118, 26 November 1996 (1996-11-26), pages 25 - 32, XP003018522
YOSHIZAWA T. ET AL.: "RNA Niji Kozo Yosoku Shien System no Kaihatsu to Jisso (Developing RNA Secondary Structure Prediction Support System)", DAI 32 KAI REPORTS OF THE MEETING OF SPECIAL INTEREST GROUP ON FUNDAMENTAL THEORY OF ARTIFICIAL INTELLIGENCE (SIG-FAI-9703) THE JAPANESE SOCIETY FOR ARTIFICIAL INGELLIGENCE, 26 March 1998 (1998-03-26), XP003018523
GULTYAEV A.P.: "The computer simulation of RNA folding involving pseudoknot formation", NUCLEIC ACIDS RESEARCH, vol. 19, no. 9, 11 May 1991 (1991-05-11), pages 2489 - 2494, XP003018524
RUAN J. ET AL.: "An Iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots", BIOINFORMATICS, OXFORD UNIVERSITY ORESS, vol. 20, no. 1, 2004, pages 58 - 66, XP003018525
MINORU KANEHISA: "Invitation to post genome information", 10 June 2001, KYORITSU SHUPPAN CO. LTD., pages: 108 - 111
YASUSHI OKAZAKI; HIDEMASA BOUNOU: "Bioinformatics: Sequence and Genome Analysis", MEDICAL SCIENCES INTERNATIONAL LTD., pages: 212 - 242
GORODKIN ET AL.: "Discovering common stem-loop motifs in unaligned RNA sequences", NUCLEIC ACIDS RESEARCH, vol. 29, no. 10, 2001, pages 2135 - 2144
See also references of EP 2012246A4
Attorney, Agent or Firm:
YAMASHITA, Johei (Toranomon 40th MT Bldg. 13-1,Toranomon 5-chome, Minato-ku, Tokyo 01, JP)
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