Development of novel methods for sequence comparison in the era of massive DNA sequencing data

2012 Fiscal Year Final Research Report

• Project/Area Number: 22310124
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: System genome science
• Research Institution: National Institute of Advanced Industrial Science and Technology (2012); Kyoto University (2010-2011)
• Principal Investigator: GOTOH Osamu 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 招聘研究員 (40142111)
• Co-Investigator(Kenkyū-buntansha): ICHINOSE Natsuhiro 京都大学, 情報研究科, 助教 (70302750)
• Project Period (FY): 2010 – 2012
• Keywords: 次世代シークエンサー / アラインメント / ゲノム / RNA-Seq / 比較ゲノム / スプライシング / アルゴリズム / アセスメント

Research Abstract

We focused on middle-to-long DNA reads generated by new generation sequencers, and developed a computer program named “Spaln” that maps and spliced-align a set of transcripts onto reference genomic sequences. When tested on full length cDNA or protein ami

Research Products

• [Journal Article] Heuristic Alignment Methods, Methods in Molecular Biology (2013)
  • Author(s): Gotoh, O
  • Journal Title: Russel, D. ed Volume: (in press)
• [Journal Article] Evolution of cytochrome P450 genes from the viewpoint of genome informatics (2012)
  • Author(s): Gotoh, O
  • Journal Title: Biol. Pharm. Bull Volume: 35 (6) Pages: 812-817
  • DOI: DOI:10.1248/bpb.35.812
  • Peer Reviewed
• [Journal Article] Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features (2012)
  • Author(s): Iwata, H. and Gotoh, O
  • Journal Title: Nucleic Acids Res Volume: 40 (20) Pages: e161
  • DOI: DOI:10.1093/nar/gks708
  • Peer Reviewed
• [Journal Article] Identification of a new clock-related element EL-box involved in circadian regulation by BMAL1/CLOCK and HES1 (2012)
  • Author(s): Ueshima, T., Kawamoto, T., Honda, K.K, Noshiro, M., Fujimoto, K., Nakao, S., Ichinose, N., Hashimoto, S., Gotoh, O., Kato, Y
  • Journal Title: Gene Volume: 510 (2) Pages: 118-125
  • DOI: DOI:10.1016/j.gene.2012.08.022
  • Peer Reviewed
• [Journal Article] A large-scale motif discovery using a DNA Gray code and equiprobable oligomers (2012)
  • Author(s): Ichinose, N., Yada, T., Gotoh, O
  • Journal Title: Bioinformatics Volume: 28 (1) Pages: 25-31
  • DOI: DOI:10.1093/bioinformatics/btr606
  • Peer Reviewed
• [Journal Article] Comparative analysis of information contents relevant to recognition of introns in many species (2011)
  • Author(s): Iwata, H. and Gotoh, O
  • Journal Title: BMC Genomics Volume: 12 Pages: 45
  • DOI: DOI:10.1186/1471-2164-12-45
  • Peer Reviewed
• [Journal Article] Cgaln: fast and space-efficient whole-genome alignment (2010)
  • Author(s): Nakato, R. and Gotoh, O
  • Journal Title: BMC Bioinformatics Volume: 11 Pages: 224
  • DOI: DOI:10.1186/1471-2105-11-224
  • Peer Reviewed
• [Presentation] Detection of splice junctions from mid-to-long RNA-seq reads by Spaln (2012)
  • Author(s): Zeng, C., Iwata, H., Ichinose, N., Yata, T., Gotoh, O
  • Organizer: GIW 2012
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
  • Year and Date: 20121212-14
• [Presentation] Mapping middle-to-long RNA-seq reads onto genomic sequence (2012)
  • Author(s): Zeng, C., Iwata, H., Gotoh, O
  • Organizer: JSBi 2012
  • Place of Presentation: タワーホール船堀, Tokyo(東京都)
  • Year and Date: 20121015-17
• [Presentation] Gene-structure-aware multiple protein sequence alignment as a tool for assessment of predicted eukaryotic gene structures (2012)
  • Author(s): Gotoh, O. and Morita, M
  • Organizer: JSBi 2012
  • Place of Presentation: タワーホール船堀, Tokyo(東京都)
  • Year and Date: 20121015-17
• [Presentation] The examination of enhanced diversity in the substrate recognition sites of P450 (2012)
  • Author(s): Morita, M. and Gotoh, O
  • Organizer: The Regional Museum of Natural Sciences - Turin
  • Place of Presentation: Torino, Italy
  • Year and Date: 20120622-26
• [Presentation] Comparison of two strategies for comprehensive identification of P450 genes on multiple eukaryotic genomes, Cytochrome P450 Biodiversity and Biotechnology (2012)
  • Author(s): Gotoh, O. and Morita, M
  • Organizer: The Regional Museum of Natural Sciences -Turin
  • Place of Presentation: Torino, Italy
  • Year and Date: 20120622-26
• [Presentation] Evaluation of Spliced Alignment Programs using Cross-Species Benchmark Datasets (2011)
  • Author(s): Iwata, H. and Gotoh, O
  • Organizer: JSBi 2010
  • Place of Presentation: 神戸国際会議場, Kobe(兵庫県)
  • Year and Date: 20110000
• [Presentation] 配列アラインメントのこれまでとこれから (2011)
  • Author(s): 後藤修
  • Organizer: CBI/JSBi 合同大会
  • Place of Presentation: 神戸国際会議場, 神戸(兵庫県)
  • Year and Date: 2011-11-10
• [Presentation] ゲノム上の分布から見た P450 遺伝子族の進化 (2011)
  • Author(s): 後藤 修
  • Organizer: 日本生化学会
  • Place of Presentation: 京都国際会議場(京都府)
  • Year and Date: 2011-09-24
• [Presentation] Evaluation of Spliced Alignment Programs Including an Extended Version of Spaln (2010)
  • Author(s): Iwata, H. and Gotoh, O
  • Organizer: JSBi
  • Place of Presentation: 九州大学医学部百年講堂, Fukuoka(福岡県)
  • Year and Date: 20101213-15
• [Presentation] Memory Management of Pairwise Alignment Using Garbage Collection (2010)
  • Author(s): Ichinose, N., Yada, T. and Gotoh, O
  • Organizer: JSBi
  • Place of Presentation: 九州大学医学部百年講堂,, Fukuoka(福岡県)
  • Year and Date: 20101213-15
• [Presentation] RDF Curator: A Novel Workflow that Generates Semantic Graph from Literature for Curation Using Text Mining (2010)
  • Author(s): Komiyama, Y. and Gotoh, O
  • Organizer: Proc. Biocuration 2010,International Society for Biocuration
  • Place of Presentation: AIST Waterfront Bio-IT Research Building, Tokyo(東京都)
  • Year and Date: 20101011-14
• [Presentation] A Method for fast and space-efficient whole-genome sequence alignment, in Proceeding of the 5th International Conference (2010)
  • Author(s): Nakato, R. and Gotoh, O
  • Organizer: "Genomics, Proteomics, Bioinformatics and Nanobiotechnology for Medicine" GPBNM-2010
  • Place of Presentation: St. Petersburg, Russia
  • Year and Date: 20100531-0605
• [Presentation] Comparative analysis of information contents relevant to intron recognition in many species (2010)
  • Author(s): Iwata, H. and Gotoh, O
  • Organizer: 3rd Asian Young Researchers Conference for Computational and Omics Biology
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
  • Year and Date: 20100310-12
• [Presentation] A Related Graph Generation System for Biomass Data and Its Evaluation by Comparison with Manual Curation (2010)
  • Author(s): Komiyama, Y. and Gotoh, O
  • Organizer: JSBi
  • Place of Presentation: Fukuoka(福岡県)
  • Year and Date: 20100000
• [Book] バイオインフォマティクス (2011)
  • Author(s): 後藤修
  • Publisher: シュプリンガージャパン
• [Remarks]
  • URL: http://www.genome.ist.i.kyoto-u.ac.jp/aligner.php