Development of computational methods for comparing a large scale multiple genome sequences

2009 Fiscal Year Final Research Report

• Project/Area Number: 17018029
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Keio University
• Principal Investigator: SAKAKIBARA Yasubumi Keio University, 理工学部, 教授 (10287427)
• Co-Investigator(Kenkyū-buntansha): ASAI Kiyoshi 東京大学, 新学術領域創成科学研究科, 教授 (30356357)
• Project Period (FY): 2005 – 2009
• Keywords: 比較ゲノム / マルチプルアライメント / ゲノム再編成 / 2次構造予測 / 機能性RNA / アセンブリ

Research Abstract

We have developed a genome comparison algorithm, named Murasaki, makes it possible to identify well-conserved regions within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Murasaki can perform a sensitive alignment of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass comparison algorithm for multiple mammalian genomes.

Research Products

• [Journal Article] Genome-wide searching with base-pairing kernel functions for non-coding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans (2009)
  • Author(s): Morita, M., Saito, Y., Sato, K., Oka, K., Hotta, K., Sakakibara, Y.
  • Journal Title: Nucleic Acids Research 37(3) Pages: 999-1009
  • Peer Reviewed
• [Journal Article] Accurate identification of orthologous segments among multiple genomes (2009)
  • Author(s): Hachiya, T., Osana, Y., Popendorf, K., Sakakibara, Y.
  • Journal Title: Bioinformatics 25(7) Pages: 853-860
  • Peer Reviewed
• [Journal Article] Integrating statistical predictions and experimental Verifications for enhancing protein-chemical interaction predictions in virtual screening (2009)
  • Author(s): Nagamine, N., Shirakawa, T., Minato, Y., Torii, K., Kobayashi, H., Imoto, M., Sakakibara, Y.
  • Journal Title: PLoS Computational Biology 5(6) Pages: 1000397
  • Peer Reviewed
• [Journal Article] Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions (2009)
  • Author(s): Akama, T., Suzuki, K., Tanigawa, T., Kawashima, A., Wu, H., Nakata, N., Osana, Y., Sakakibara, Y., Ishii, N.
  • Journal Title: Journal of Bacteriology 191 Pages: 3321-3327
  • Peer Reviewed
• [Journal Article] Prediction of RNA secondary structure by combining homologous sequence information (2009)
  • Author(s): Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.
  • Journal Title: Bioinformatics 25(12) Pages: 330-338
  • Peer Reviewed
• [Journal Article] CENTROIDFOLD: a web server for RNA secondary structure prediction (2009)
  • Author(s): Sato, K., Hamada, M., Asai, K., Mituyama, T.
  • Journal Title: Nucleic Acids Res. 37(Web Server issue) Pages: W277-W280
  • Peer Reviewed
• [Journal Article] A local multiple alignment method for detection of non-coding RNA sequences (2009)
  • Author(s): Tabei, Y., Asai, K.
  • Journal Title: Bioinformatics 25(12) Pages: 1498-1505
  • Peer Reviewed
• [Journal Article] A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila (2009)
  • Author(s): Saito, K., Inagaki, S., Mituyama, T., Kawamura, Y., Ono, Y., Sakota, E., Kotani, H., Asai, K., Siomi, H., Siomi, M.C.
  • Journal Title: Nature 461(7268) Pages: 1296-1299
  • Peer Reviewed
• [Journal Article] CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score (2009)
  • Author(s): Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.
  • Journal Title: Bioinformatics (Advance Access)
  • Peer Reviewed
• [Journal Article] Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation (2009)
  • Author(s): Kikuchi, K., Fukuda, M., Ito, T., Inoue, M., Yokoi, T., Chiku, S., Mitsuyama, T., Asai, K., Hirose, T., Aizawa, Y.
  • Journal Title: Nucleic Acids Res. 35(15) Pages: 4987-5000
  • Peer Reviewed
• [Journal Article] PSSMTS: position specific scoring matrices on tree structures (2008)
  • Author(s): Sato, K., Morita, K., Sakakibara, Y.
  • Journal Title: Journal of Mathematical Biology 56 Pages: 201-214
  • Peer Reviewed
• [Journal Article] Directed acyclic graph kernels for structural RNA analysis (2008)
  • Author(s): Sato, K., Mituyama, T., Asai, K., Sakakibara, Y.
  • Journal Title: BMC Bioinformatics 9 Pages: 318
  • Peer Reviewed
• [Journal Article] Rfold: An exact algorithm for computing local base pairing probabilities (2008)
  • Author(s): Kiryu, H., Kin, T., Asai, K.
  • Journal Title: Bioinformatics 24(3) Pages: 367-373
  • Peer Reviewed
• [Journal Article] A fast structural multiple alignment method for long RNA sequences (2008)
  • Author(s): Tabei, Y., Kiryu, H., Kin, T., Asai, K.
  • Journal Title: BMC Bioinformatics 9 Pages: 33
  • Peer Reviewed
• [Journal Article] Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates (2008)
  • Author(s): Okada, K., Asai, K.
  • Journal Title: Gene 412(1-2) Pages: 71-83
  • Peer Reviewed
• [Journal Article] Software. ncrna. org: web servers for analyses of RNA sequences (2008)
  • Author(s): Asai, K, Kiryu, H, Hamada, M, Tabei, Y, Sato, K, Matsui, H, Sakakibara, Y, Terai, G,, Mituyama, T.
  • Journal Title: Nucleic Acids Res. 36 Pages: W75-8
  • Peer Reviewed
• [Journal Article] Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells (2008)
  • Author(s): Kawamura, Y, Saito, K, Kin, T, Ono, Y, Asai, K, Sunohara, T, Okada, T. N, Siomi, M. C,, Siomi, H.
  • Journal Title: Nature 453(7196) Pages: 793-797
  • Peer Reviewed
• [Journal Article] Expansion of signaling genes for adaptive immune system evolution in early vertebrates (2008)
  • Author(s): Okada, K,, amd Asai, K
  • Journal Title: BMC Genomics 9 Pages: 218
  • Peer Reviewed
• [Journal Article] Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing (2008)
  • Author(s): Azuma-Mukai, A, Oguri, H, Mituyama, T, Qian, Z. R, Asai, K, Siomi, H,, Siomi, M.C.
  • Journal Title: PNAS 105(23) Pages: 7964-7969
  • Peer Reviewed
• [Journal Article] Prediction of RNA secondary structure using generalized centroid estimators (2008)
  • Author(s): Hamada, M., Kiryu, H., Sato, K., Mituyama, T., Asai, K.
  • Journal Title: Bioinformatics 25(4) Pages: 465-73
  • Peer Reviewed
• [Journal Article] Stem kernels for RNA sequence analyses (2007)
  • Author(s): Sakakibara, Y., Ogawa, N., Popendorf, K., Asai, K., K. Sato
  • Journal Title: Journal of Bioinformatics and Computational Biology 5(6) Pages: 1103-1122
  • Peer Reviewed
• [Journal Article] Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data (2007)
  • Author(s): Nagamine, N., Sakakibara, Y.
  • Journal Title: Bioinformatics 23(15) Pages: 2004-2012
  • Peer Reviewed
• [Journal Article] Robust prediction of consensus secondary structures using averaged base pairing probability matrices (2007)
  • Author(s): Kiryu, H., Kin, T., Asai, K.
  • Journal Title: Bioinformatics 23(13) Pages: 1588-1598
  • Peer Reviewed
• [Journal Article] Murlet: A practical multiple alignment tool for structural RNA sequences (2007)
  • Author(s): Kiryu, H., Tabei, Y., Kin T., Asai, K.
  • Journal Title: Bioinformatics 23(13) Pages: 1588-1598
  • Peer Reviewed
• [Journal Article] miRRim: A novel system to find conserved miRNAs with high sensitivity and specificity (2007)
  • Author(s): Terai, G., Komori, T., Asai, K., Kin, T.
  • Journal Title: RNA 13 Pages: 2081-2090
  • Peer Reviewed
• [Journal Article] SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments (2006)
  • Author(s): Tabei, Y., Tsuda, K., Kin, T., Asai, K.
  • Journal Title: Bioinformatics 22(14) Pages: 1723-1729
  • Peer Reviewed
• [Journal Article] Mining frequent stem patterns from unaligned RNA sequences (2006)
  • Author(s): Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.
  • Journal Title: Bioinformatics 22(20) Pages: 2480-2487
  • Peer Reviewed
• [Journal Article] Grammatical Inference in Bioinformatics (2005)
  • Author(s): Sakakibara, Y.
  • Journal Title: IEEE Transactions on Pattern Analysis and Machine Intelligence 27(7) Pages: 1051-1062
  • Peer Reviewed
• [Journal Article] Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures (2005)
  • Author(s): atsui, H., Sato, K., Sakakibara, Y.
  • Journal Title: Bioinformatics 21(11) Pages: 2611-2617
  • Peer Reviewed
• [Journal Article] RNA secondary structural alignment with conditional random fields (2005)
  • Author(s): Sato, K., Sakakibara, Y.
  • Journal Title: Bioinformatics 21(Suppl.2) Pages: 237-242
  • Peer Reviewed
• [Journal Article] Identifying cooperative transcriptional regulations using protein-protein interactions (2005)
  • Author(s): Nagamine, N., Kawada, Y., Sakakibara, Y.
  • Journal Title: Nucleic Acids Research 33(15) Pages: 4828-4837
  • Peer Reviewed
• [Journal Article] Genome sequencing and analysis of Aspergillus oryzae (2005)
  • Author(s): Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, et al.
  • Journal Title: Nature 438(7071) Pages: 1057-1161
  • Peer Reviewed
• [Presentation] Gradient-based optimization of hyperparamers for base-pairing profile local alignment kernels (2009)
  • Author(s): Sato, K., Saito, Y., Sakakibara, Y.
  • Organizer: Genome Informatics
  • Place of Presentation: Yokohama, Japan
  • Year and Date: 2009-12-14
• [Presentation] A non-parametric Bayesian approach for predicting RNA secondary structures (2009)
  • Author(s): Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
  • Organizer: Proceedings of 9th Workshop on Algorithms in Bioinformatics (WABI 2009)
  • Place of Presentation: Philadelphia, USA
  • Year and Date: 2009-09-12
• [Presentation] Detection of Secondary-Structure Conserved Regions by Genome Comparison (2008)
  • Author(s): Saito, Y., Sato, K., Sakakibara, Y.
  • Organizer: The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi 2008)
  • Place of Presentation: Osaka, Japan(口頭発表)
  • Year and Date: 2008-12-16
• [Presentation] OSfinder: an accurate orthology mapping program and its application to placental mammalian genomes (2007)
  • Author(s): Hachiya, T., Osana, Y., Popendorf, K., Sakakibara, Y.
  • Organizer: Proc. 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi 2007)
  • Place of Presentation: Tokyo, Japan
  • Year and Date: 2007-12-18
• [Presentation] Stem Kernels for RNA Sequence Analyses (2007)
  • Author(s): Sakakibara, Y., Asai, K., Sato, K.
  • Organizer: Proc. 1st International Conference on Bioinformatics Research and Development
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2007-03-13
• [Presentation] Detection of Cis-Acting Regulatory Variation from Location Data (2006)
  • Author(s): Kawada, Y., Sakakibara, Y.
  • Organizer: Proceedings of the 4th Asia-Pacific Bioinformatics Conference (APBC 2006)
  • Place of Presentation: Taiwan, China
  • Year and Date: 2006-02-14
• [Presentation] Searching biologically plausible synteny blocks among multiple genomes (2005)
  • Author(s): Hachiya, T., Sakakibara, Y.
  • Organizer: BIOINFO 2005 (proceedings of 2005 International Joint Conference of InCoB, AASBi and KSBI)
  • Place of Presentation: Busan, Korea
  • Year and Date: 2005-09-22
• [Remarks] Popendorf, K., Osana, Y., and Sakakibara, Y., 比較ゲノム解析システムMurasaki, ソフトウエア(バージョン1. 35 )
  • URL: http://murasaki.dna.bio.keio.ac.jp/
• [Remarks] Asai, K,, Kiryu, H,, Hamada, M,, Tabei, Y,, Sato, K,, Matsui, H,, Sakakibara, Y,, Terai, G,, and Mituyama, T., rna配列解析統合ウェブサーバ
  • URL: http://software.ncrna.org/