1.[SCARNA]
Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai:
"SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments,"
Bioinformatics 2006 22(14):1723-1729; doi:10.1093/bioinformatics/btl177
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2.[Murlet]
Hisanori Kiryu, Yasuo Tabei, Taishin Kin, and Kiyoshi Asai:
"Murlet: A practical multiple alignment tool for structural RNA sequences,"
Bioinformatics 2007 23(13): 1588-1598; doi:10.1093/bioinformatics/btm146
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3.[MXSCARNA]
Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai:
"A fast structural multiple alignment method for long RNA sequences,"
BMC Bioinformatics 2008, 9:33 doi:10.1186/1471-2105-9-33
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4.[RNAmine]
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, and Kiyoshi Asai:
"Mining frequent stem patterns from unaligned RNA sequences,"
Bioinformatics 2006 22(20):2480-2487; doi:10.1093/bioinformatics/btl431
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5.[PHMMTS]
Sakakibara Y.:
Pair Hidden Markov Models on Tree Structures, Bioinformatics vol.19, suppl.1, pp.i232-40, 2003
6.[PSTAG]
Matsui, H, Sato, K. and Sakakibara, Y.:
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures, Bioinformatics, vol.21, no.11, pp.2611-2617, 2005
7.[SOCOS/CAN]
Taishin Kin, Koji Tsuda and Kiyoshi Asai:
"Marginalized Kernels for RNA Sequence Data Analysis,"
Genome Informatics Vol.13, 112-122
(GIW2002 Best Paper Award, 2002).
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8.[Stem Kernel]
Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai and Kengo Sato:
"Stem Kernels for RNA Sequence Analyses,"
Journal of Bioinformatics and Computational Biology 2007 Oct;5(5): 1103-22.
9.[miRRim]
Goro Terai, Takashi Komori, Kiyoshi Asai and Taishin Kin:
"miRRim: A novel system to find conserved miRNAs with high sensitivity and specificity,"
RNA 2007 13:2081-2090. Published in Advance October 19, 2007, doi:10.1261/rna.655107
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10.[McCaskill-MEA]
Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai:
"Robust prediction of consensus secondary structures using averaged base pairing probability matrices,"
Bioinformatics 2007 23(4):434-441; doi:10.1093/bioinformatics/btl636
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11.[Rfold]
Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai:
"Rfold: An exact algorithm for computing local base pairing probabilities,"
Bioinformatics Advance Access published on December 4, 2007.
doi:10.1093/bioinformatics/btm951
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