GIW ’98
The Ninth Workshop on Genome Informatics
Yebisu Garden Hall
Yebisu Garden Place, Tokyo, Japan
December 10-11, 1998
The Ninth Workshop on Genome Informatics (GIW ’98) is a forum for researchers,
practitioners and users working on various aspects of Genome Informatics. The aim
is to present recent research results (theory/practice), to demonstrate systems, and to
explore directions for future research and new applications related to Genome Science.

Steering Committee
Minoru Kanehisa (Chair, Kyoto University)
Toshihisa Takagi (University of Tokyo)
Satoru Miyano (University of Tokyo)

Sponsored by
Human Genome Center, University of Tokyo
Grant-in-Aid for Scientific Research on Priority Areas“GENOME SCIENCE” from MESSC of Japan

Secretary and Local Arrangements
giw@ims.u-tokyo.ac.jp
Human Genome Center
Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Tel:+81-3-5449-5615
Fax:+81-3-5449-5442

Newest Information
http://www.hgc.ims.u-tokyo.ac.jp/giw98

1

Program Committee
Toshihisa Takagi (Chair, U. Tokyo, Japan)
Kiyoshi Asai (ETL, Japan)
Peer Bork (EMBL, Germany)
Christopher Burge (MIT, USA)
Antoine Danchin (Institut Pasteur, France)
A. Keith Dunker (Washington State Univ., USA)
Susumu Goto (Kyoto University, Japan)
Philip P. Green (U. Washington, USA)
Lawrence Hunter (National Library of Medicine, USA)
Takashi Ito (University of Tokyo, Japan)
Hiroaki Kitano (SONY, Japan)
Akihiko Konagaya (JAIST, Japan)
Satoru Kuhara (Kyushu University, Japan)
Hideo Matsuda (Osaka University, Japan)
Satoru Miyano (Chair, University of Tokyo, Japan)
Shin-ichi Morishita (University of Tokyo, Japan)
Kenta Nakai (Osaka University, Japan)
Naotake Ogasawara (AIST-Nara, Japan)
Christos Ouzounis (EMBL-EBI, U.K.)
Ross Overbeek (ANL, USA)
Gary D. Stormo (University of Colorado, USA)
Hideaki Sugawara (DDBJ, Japan)
Satoshi Tabata (KDRI, Japan)
Michael S. Waterman (U. Southern California, USA)
Limsoon Wong (NUS, Singapore)

Advanced Registration
The registration fee is free except the banquet (6,000 Yen; 3,000 Yen for student) andthe workshop book (3,000 Yen).
Registration to GIW ’98 can be done at the above URL site, or please send yourname, affiliation, email address, phone number, fax number, banquet attendance, tothe secretary.

GIW ’98 Advanced Program
Registration
From 9:00 at Yebisu Garden Hall on December 10 and 11. (Registration Desk is open from through the workshop.)

December 10, Thursday
Opening Address
9:50 - 10:00
Toshihisa Takagi (Univ. Tokyo)
Session 1
10:00 - 10:20

Chair: Kenta Nakai (Osaka Univ.)
Genomic Analysis of the Genes Encoding Ribosomal Proteins inEight Eubacterial Species and Saccharomyces cerevisiae , Katsutoshi Fujita∗ , Tomoya Baba† , Katsumi Isono∗ (∗ Kobe Univ.,†
STAFF)

10:20 - 10:40

Construction of the gyrB Database for the Identification andClassification of Bacteria, Hiroaki Kasai∗ , Kanako Watanabe∗ ,Elizabeth Gasteiger† , Amos Bairoch† , Katsumi Isono‡ , Satoshi
Yamamoto§ , Shigeaki Harayama∗ (∗ Marine Biotech. Inst.,†
Univ. Geneva, Switz., ‡ Kobe Univ., § Nichirei Corp.)

10:40 - 11:00

Philogenetic Invariants for Metazoan Mitochondrial Genome
Evolution, David Sankoff∗ and Mathieu Blanchette† (∗ Univ.
Montreal, Canada, † Univ. Washington, USA)

11:00 - 11:20

Systematic Prediction of Orthologous Units of Genes in the
Complete Genomes, Hidemasa Bono, Susumu Goto, Wataru Fujibuchi, Hiroyuki Ogata, Minoru Kanehisa (Kyoto Univ.)

11:20 - 11:40

Comprehensive Sequence Analyses of 5’ Flanking Regions ofPrimate Alu elements, Yoshimi Toda, Rintaro Saito, Masaru
Tomita (Keio Univ.)

11:40 - 12:00

Evidence of Limited Structural Organization in Globin Intron
Sequences of Messenger RNA, Wayne Dawson and Kenji Yamamoto (Univ. Tokyo)

Lunch BreakInvited Talk
13:30 - 14:30

Coffee Break

12:00 - 13:30
Chair: Hiroshi Imai (Univ. Tokyo)
Information Geometry and Neural Networks, Shun-ichi Amari(RIKEN Brain Science Institute)
14:30 - 14:40

Session 2
14:40 - 15:00

Chair: Christos Ouzounis (EMBL-EBI, UK)
Identifying the Interaction between Genes and Gene Products
Based on Frequently Seen Verbs in Medline Abstracts, Takeshi
Sekimizu, Hyun S. Park, Jun’ichi Tsujii (Univ. Tokyo)

15:00 - 15:20

Detecting Gene Symbols and Names in Biological Texts : A
First Step toward Pertinent Information Extraction, Denys
Proux∗ , François Rechenmann† , Laurent Julliard∗ , Violaine
Pillet‡ , Bernard Jacq§ (∗ Xerox Research Centre Europe, France,†
INRIA Rhône-Alpes, France, ‡ CRRM, France, § LGPD, France)

15:20 - 15:40

Developing NLP Tools for Genome Informatics: An Information Extraction Perspective, Teruyoshi Hishiki, Nigel Collier, Chikashi Nobata, Tomoko Okazaki-Ohta, Norihiro Ogata,
Takeshi Sekimizu, Roland Steiner, Hyun S. Park, Jun’ichi Tsujii(Univ. Tokyo)

15:40 - 16:00

A Machine Learning Approach to Reducing the Work of Experts
in Article Selection from Database: A Case Study for Regulatory Relations of S. cerevisiae Genes in MEDLINE, Shin-ichi
Usuzaka∗ , Kim Lan Sim† , Miyako Tanaka‡ , Hiroshi Matsuno∗ ,Satoru Miyano† (∗ Yamaguchi Univ., † Univ. Tokyo, ‡ Ube Natl.
Coll. of Tech.)Posters & Software Demonstrations
Chair: Shigeki Mitaku (Tokyo Univ. ofAgriculture and Tech.)
16:00 - 18:30
Banquet18:30 - 21:00
Foyer, Garden Hall

December 11, Friday
Session 3
9:30 - 9:50

Chair: Hideo Matsuda (Osaka Univ.)
Using Kleisli to Bring Out Features in BLASTP Results, Jing
Chen, Daphna Strauss, Limsoon Wong (Kent Ridge DigitalLab., Singapore)

9:50 - 10:10

MUSCA: An Algorithm for Constrained Alignment of Multiple
Data Sequences, Laxmi Parida, Aris Floratos, Isidore Rigoutsos(IBM T.J.Watson Research Center, USA)

10:10 - 10:30

Improvement of the A∗ Algorithm for Multiple Sequence Alignment, Hirotada Kobayashi and Hiroshi Imai (Univ. Tokyo)

10:30 - 10:50

Parallel Protein Information Analysis (PAPIA) System Runningon a 64-Node PC Cluster, Yutaka Akiyama, Kentaro Onizuka,
Tamotsu Noguchi, Makoto Ando (RWCP)

Coffee Break

10:50 - 11:00

Invited Talk
11:00 - 12:00

Lunch Break

Chair: Naotake Ogasawara (AIST-Nara)
Comparative Genomics: Is It Changing the Paradigm of Evolutionary Biology?, Eugene V. Koonin (NIH, USA)
12:00 - 13:00

Posters & Software Demonstrations
13:30 - 15:00

Session 4
15:00 - 15:20

Chair: Takashi Ito (Univ. Tokyo)
Finding Genetic Network from Experiments by Weighted Network Model, Kiyoshi Noda∗ , Ayumi Shinohara∗ , Masayuki
Takeda∗ , Satoshi Matsumoto† , Satoru Miyano‡ , Satoru Kuhara∗(∗ Kyushu Univ. † Tokai Univ. ‡ Unvi. Tokyo)

15:20 - 15:40

A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions, Tatsuya Akutsu∗ , Satoru Kuhara† , Osamu Maruyama∗ ,Satoru Miyano∗ (∗ Univ. Tokyo † Kyushu Univ.)

15:40 - 16:00

Fully-Automated Spot Recognition and Matching Algorithms
for 2-D Gel Electrophoretogram of Genomic DNA, Katsutoshi
Takahashi∗ , Masayuki Nakazawa† , Yasuo Watanabe‡ , Akihiko
Konagaya∗ (∗ JAIST, † IPC, ‡ Kanazawa Inst. of Tech.)

Coffee Break

16:00 - 16:20

Session 5
16:20 - 16:40

Chair: Satoru Kuhara (Kyushu Univ.)
Hunting TPR Domains Using Kleisli, Kui Lin∗ , Anthony E.
Ting† , Jiren Wang‡ , Limsoon Wong‡ , (∗ National Univ. of Singapore, † Inst. of Molecular & Cell Biol., Singapore, ‡ Kent Ridge
Digital Labs., Singapore)

16:40 - 17:00

Low Identity, Low Similarity Protein Sequences: Independent
Modeling of the Ordered-Series-of-Motifs and Motif-InterveningRegions, Marcella A. McClure, Julianna Hudak, John Kowalski(UNLV, USA)

17:00 - 17:20

The Sequence Attribute Method for Determining Relationships
Between Sequence and Protein Disorder, Qian Xie∗ , Gregory
E. Arnold† , Pedro Romero∗ , Zoran Obradovic∗ , Ethan Garner∗ ,A. Keith Dunker∗ (∗ Washington State Univ., USA, † Biol. Info.
Tech., USA)

17:20 - 17:40

Predicting Disordered Regions from Amino Acid Sequence:
Common Themes Despite Differing Structural Characterization,
Ethan Garner, Paul Cannon, Pedro Romero, Zoran Obradovic,
A. Keith Dunker (Washington State Univ., USA)

Closing
Remarks

17:40 - 17:50
Kiyoshi Asai (ETL)Software Demonstrations
S1: Mobile Agent System for Animal Genome Database, Yasuhiko Wada∗ , Hirohisa
Kishino† , Nobuhisa Kashiwagi‡ , Hiroshi Yasue∗ , (∗ NIAI, † Inst. of Statistical
Math., ‡ Univ. Tokyo)
S2: A Sample Tracking Tool for Rice Genome Sequencing, Katsumi Sakata∗ , Kazunori
Waki∗ , Takuji Sasaki∗ , Michihiko Shimomura† , Masaki Kise† (∗ NIAR/STAFF,†
Mitsubishi Space Software Co., Ltd.)S3: NEXTDB: The Expression Pattern Map Database for C. elegans, Tadasu Shin-i,
Yuji Kohara (NIG)
S4: Constructing and Annotating GENES Database in KEGG, Susumu Goto∗ , Kotaro Shiraishi† , Kayo Okamoto∗ , Hiroko Ishida∗ , Sanae Asanuma∗ , Hidemasa
Bono∗ , Hiroyuki Ogata∗ , Wataru Fujibuchi∗ , Minoru Kanehisa∗ (∗ Kyoto Univ.,†
Fujitsu Kyushu System Eng.)S5: ORI-GENE: A Tool for Gene Classification Based on Evolutional Tree, Hideaki
Mizuno∗ , Yoshimasa Tanaka∗ , Yoshihiro Ugawa† , Akinori Sarai‡ (∗ Univ. of
Tsukuba, † NIAR, ‡ RIKEN)
S6: Genome-Scale Gene Expression Profiles Mapped onto the Pathway and Genome
Maps in KEGG, Mitsuteru Nakao∗ , Kazushige Sato† , Tomomi Kamiya∗ , Yoshiko
Kimura∗ , Minoru Kanehisa∗ (∗ Kyoto Univ., † Nihon SiliconGraphics K.K.)
S7: Virtual Drosophila Project: Simulation of Drosophila Leg Formation, Koji Kyoda∗ ,Hiroaki Kitano† (∗ Keio Univ., † Sony Computer Sci. Lab., Inc.)
S8: KMeyeDB: Keio Mutation Database for Eye Disease Genes Constructed on a
Graphical Distributed Database System Mutation View, Shinsei Minoshima,
Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu (KeioUniv.)
S9: GeneWeb II: Sequence Analysis Tools on Web Server Using Java API, Ken
Kurokawa∗ , Kenichi Kawashima† , Toshiyuki Okumura† , Tatsuya Takagi∗ , Teruo
Yasunaga∗ (∗ Osaka Univ., † Senri Life Sci. Center)
S10: Parallelized Knowledge Discovery System: An Enhancement to BONSAI, Hideo
Bannai∗ , Toshio Masuda† , Masao Nagasaki∗ , Tomohiro Yasuda∗ , Osamu Maruyama∗ ,Satoru Miyano∗ (∗ Univ. Tokyo, † Graduate School of Electro-Comm.)

Posters
P01: Annotation of PDB with respect to “Disordered Regions” in Proteins, Meeta
Rani∗ , Pedro Romero† , Zoran Obradovic† , A. Keith Dunker† (∗ Natl. Univ.
Singapore, † Washington State Univ., USA)
P02: E-CELL Project Overview:Towards Integrative Simulation of Cellular Processes,
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Yuri Matsuzaki, Ryo
Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano,
Sakura Tanida, Thomas S. Shimizu (Keio Univ.)
P03: Modeling of Transcription and DNA Replication Using the E-CELL Simulation System, Kenta Hashimoto, Fumihiko Miyoshi, Thomas S. Shimizu, Takeshi
Satoyoshi, Masaru Tomita (Keio Univ.)
P04: Modeling of Signal Transduction for Bacterial Chemotaxis Using the E-CELL
Simulation System, Yuri Matsuzaki, Kanako Saito, Tom Shimizu, Masaru Tomita(Keio Univ.)
P05: Modeling of Human Red Blood Cell Using the E-CELL Simulation System, Riou
Matsushima, Akiko Kawase, Naoko Watanabe, Hisako Nakano, Kanako Saito,
Masaru Tomita (Keio Univ.)
P06: Modeling Theory and Software Architecture of the E-CELL Simulation System,
Kouichi Takahashi, Tom Shimizu, Katsuyuki Yugi, Masaru Tomita (Keio Univ.)
P07: Multivariate Time Series Analysis of Metabolic Network Using the E-CELL
Simulation System, Yusuke Saito, Kouichi Takahashi, Masaru Tomita (KeioUniv.)
P08: Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae, Yoko Fukuda, Takanori Washio, Masaru
Tomita (Keio Univ.)
P09: On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes, Masahiko
Wada, Yukihiro Kawashima, Masaru Tomita (Keio Univ.)
P10: Computer Analysis of Base Pairing Free-Energy between Shine-Dalgarno Sequence and 16S rRNA in Various Procaryotes, Yuko Osada, Rintaro Saito,
Masaru Tomita (Keio Univ.)
P11: On Low Frequency of CpG Dinucleotides in Bacterial Genomes, Mami Goto,
Takanori Washio, Masaru Tomita (Keio University)
P12: Analysis of Translation Initiation Sites in the Complete Genome of Mycoplasma
genitalium Suggests That This Bacterium Uses Alternative Signal for Translation Initiation, Rintaro Saito, Masaru Tomita (Keio Univ.)
P13: Expression Frequency of the Human Immunoglobulin λ Light Chain Genes andthe Roles of Their Recombination Signal and Spacer Sequences, Taku Okada,
Masaru Tomita, Kazuhiko Kawasaki, Shinsei Minoshima, Nobuyoshi Shimizu(Keio Univ.)
P14: Assessment of Utility of ESTs for Nucleotide Diversity Using Available Assembled Alignments from dbESt, STACK 2.0 and STACK-INDEX, Brian Karlak,
Winston Hide (Univ. of the Western Cape, South Africa)P15: A Genome-Level Search for Bacterial Genes on Which Positive Selection May
Operate: A Means for Identifying Possible Virulence Factors?, Junaid Gamieldien, Winston Hide (Univ. of the Western Cape, South Africa)
P16: A Statistical Model for Prokaryotic Promoter Prediction, Joseph Oppon, Winston Hide (Univ. of the Western Cape, South Africa)
P17: Algorithms for Inference of Genetic Networks (AIGNET), Shoji Watanabe∗ ,Yukihiro Maki∗ , Yukihiro Eguchi∗ , Daisuke Tominaga† , Masahiro Okamoto† (∗ Mitsui
Knowledge Ind. Co., Ltd., † Kyushu Inst. of Tech.)P18: An Educational Tool for Visualize DNA Structures in vivo, Shigehiro Fukase∗ ,Masato Wayama† (∗ Hitachi Software Eng. Co., Ltd., † Biz. Service Corp.)
P19: Extended Sequence Alignment Method for Protein Secondary Structure Prediction, Susumu Hiraoka (Hitachi, Ltd.)
P20: Detection of Frame-Shift Error in the Yeast Genome Sequences, Naoko Kasahara, Naoyuki Harada, Keiichi Nagai (Hitachi, Ltd.)
P21: Clustering and Detection of 5’Splice Sites of mRNA by k Weight Matrix Model,
Katsuhiko Murakami∗ , Toshihisa Takagi† (∗ Hitachi, Ltd., † Univ. Tokyo)
P22: Automated Metabolic Reconstruction at the Molecular Level, Masanori Arita(Univ. Tokyo)
P23: Correlation between Exon and Dispersed Repetitive DNA Distributions on the
Human Genome, Yoshiaki Hojo, Ikuo Uchiyama, Yataro Daigo, Yusuke Nakamura, Toshihisa Takagi (Univ. Tokyo)
P24: Automatic Construction of Biological Abbreviation Dictionary from Abstracts ofBiomedical Papers, Mikio Yoshida, Kenichiro Fukuda, Toshihisa Takagi (Univ.
Tokyo)
P25: A Workbench for Systematic Construction of Signal Transduction Pathways:
Ontologies and Architectures, Kenichiro Fukuda, Mikio Yoshida, Toshihisa Takagi (Univ. Tokyo)
P26: Development of Information Extraction Tool: Toward Construction of ProteinProtein Interaction Database, Tomoko Okazaki-Oota, Toshihisa Takagi (Univ.
Tokyo)
P27: Palindrome Analysis: Distribution of Complete-Matched Inverted Repeats witha Moderate Length Spacer, Masao Fukagawa, Tatsuhiko Tsunoda, Toshihisa
Takagi (Univ. Tokyo)
P28: Construction of Ortholog/Paralog Group Table for PTS, Takeaki Taniguchi,
Minoru Kanehisa (Kyoto Univ.)
P29: A Library of Protein-Ligand Interaction Sites for de novo Ligand Design, Kiminobu Sato, Minoru Kanehisa (Kyoto Univ.)
P30: Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping, Wataru Fujibuchi∗ , Hiroyuki Ogata∗ , Hideo Matsuda† , Minoru Kanehisa∗(∗ Kyoto Univ., † Osaka Univ.)
P31: The Construction of the Knowledge Base of Immune System, Yoshinobu Igarashi,
Minoru Kanehisa (Kyoto Univ.)

P32: Detection of Co-regulated Genes by Comparative Analysis of Microbial Genomes,
Hiroyuki Ogata, Wataru Fujibuchi, Minoru Kanehisa (Kyoto Univ.)
P33: Extracting Regulatory Signals from the Upstream Region of Co-expressed Genes
Derived from DNA Microarray Experiments, Shuichi Kawashima, Hiroyuki Ogata,
Minoru Kanehisa (Kyoto Univ.)
P34: Protein Folding Simulation and Self-Consistent Potential Functions, Fumi Takazawa,
Masaki Sasaki, Minoru Kanehisa (Kyoto Univ.)
P35: Systematic Classification of B. subtilis Genes and Construction of a Knowledge
Base to Represent Functional Information, Atsushi Ogiwara (Natl. Inst. for
Basic Biol.)
P36: Search Pathways for Secondary Metabolites Based on Genome Analysis andChemical Knowledge on Metabolism, Takaaki Nishioka∗ , Kimito Funatsu† (∗ Kyoto
Univ., † Toyohashi Univ. of Tech.)P37: A Method for Querying Complete Genomes by Viewing Them as Structured
Documents, Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto (Osaka Univ.)
P38: Maintenance of Transcription Factor DataBase TFDB by TFDB Maintenance
System, Masako Kaizawa∗ , Satoru Watanabe∗ , Takahiro Nobukuni∗, MasamiHorikoshi† , Hiroshi Handa‡ , Yoshiyuki Kuchino∗ , Takao Sekiya∗ , Hiroshi Mizushima∗(∗ NCCRI, † Exploratory Research for Advanced Tech., ‡ Grad. School of Biosci.
& Biotech.)P39: ALIS: Data Management Systems for Human Genome Sequencing, Mika Hirakawa, Kensaku Imai, Hiroko Yamaguchi, Junko Shimada, Kazuo Takehana,
Katsuji Matsumura, Takehiko Itoh, Masako Kuroda (JST)P40: Automatic cDNA classification System for Mouse Genome Project, Yoshifumi
Fukunishi, Hideaki Konno, Yoshihide Hayashizaki (RIKEN)
P41: Automated cDNA Information System for Large Scale cDNA Project, Hideaki
Konno, Yuichi Sugahara, Yoshifumi Fukunishi, Kazuhiro Shibata, Yoshihide
Hayashizaki (RIKEN)
P42: Application of the RLGS Image Analysis Tool (RAT) to the Construction of a
Genetic Linkage Map of Recombinant Inbred Strain SMXA, Yuichi Sugahara,
Yoshihide Hayashizaki (RIKEN, JST)P43: 3DinSight: An Integrated Database and Search Tool for Structure, Function andProperty of Biomolecules, Jianghong An∗ , Takao Nakama† , Yasushi Kubota† ,Akinori Sarai∗ (∗ RIKEN, † Advanced Tech. Inst. Inc.)
P44: ProTherm: Thermodynamic Database for Proteins and Mutants, M. Michael
Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira,
Akinori Sarai (RIKEN)
P45: Prediction of DNA target Sites by Regulatory Proteins Based on StructureDerived Potential, Hidetoshi Kono, Akinori Sarai (RIKEN)
P46: Genomic Hypothesis Creator: A Multi-Strategic View Creator for Sequences,
Osamu Maruyama∗ , Tomoyuki Uchida† , Takayoshi Shoudai‡ , Satoru Miyano∗(∗ Univ. Tokyo, † Hiroshima City Univ., ‡ Kyushu Univ.)P47: Development of Web Interface of Image Analysis System DDGEL for 2D Gel
Electrophoresis, Kyotetsu Kanaya∗ , Akira Ohyama∗ , Tatsuya Akutsu† , Asao
Fujiyama‡ (∗ Mitsui Knowledge Industry Co., Ltd., † Tokyo Univ., ‡ NIG)
P48: Subcubic Time Algorithms for RNA Secondary Structure Prediction, Tatsuya
Akutsu (Univ. Tokyo)
P49: ThreeTree: A New Method to Reconstruct Phylogenetic Trees, Satoshi OOta
(NIG)
P50: Efficiency of Model-Based Complexity Method for Estimating Unrooted Multifurcate Phylogenetic Tree, Fengrong Ren, Hiroshi Tanaka (Tokyo Medical and
Dent. Univ.)
P51: Secondary Structure Prediction Based on Statistical Mechanics, Yukio Kobayashi∗ ,Nobuhiko Saitô† (∗ Soka Univ., † Waseda Univ.)
P52: Integrating Multiple Evidences by Hidden Markov Models, Kiyoshi Asai∗ , Katunobu
Itou∗ , Tetsushi Yada† (∗ ETL, † Mitsubishi Research Inst.)
P53: Modeling Transcriptional Units of E. coli Genes Using HMM, Tetsushi Yada∗ ,Mitsuteru Nakao† , Yasushi Totoki‡ , Takahiro Ishii§ , Kenta Nakai§ (∗ Mitsubishi
Research Inst., † Kyoto Univ., ‡ Info. & Math. Sci. Lab., Inc., § Osaka Univ.)
P54: A Database of B. subtilis Promoters and Transcription Factors, Takahiro Ishii,
Kenta Nakai (Osaka Univ.)
P55: A Study Using Sequence Comparison to Investigate the Molecular Evolutionof Mitochondrial tRNA Genes, Jun-Ichi Sagara, Shugo Nakamura, Mitsunori
Ikeguchi, Kentaro Shimizu (Univ. Tokyo)
P56: Prediction of Initiation Codons in cDNA Fragments Using Statistical Information and Similarity with Protein Sequences, Tetsuo Nishikawa, Toshio Ota,
Takao Isogai (Helix Research Inst.)
P57: Genome Analysis: Assigning Protein Coding Regions to 3D Structures, Asaf
A. Salamov∗ , Makiko Suwa∗ , Christine A. Orengo† , Mark B. Swindells∗ (∗ Helix
Research Inst., † Univ. Coll. London, UK)
P58: A Novel Application of GeneMark-RC to the Analysis of Prokaryotic Genomesand Human cDNAs: Sequence Data with Statistical Deviations Are Rich inImportant Biological Information, Makoto Hirosawa∗ , Osamu Ohara∗ , Katsumi
Isono† (∗ Kazusa DNA Research Inst., † Kobe Univ.)
P59: Annotation and Presentation Systems for Arabidopsis Genome Sequencing Projectat Kazusa DNA Research Institute, Yasukazu Nakamura, Shusei Sato, Satoshi
Tabata (Kazusa DNA Research Inst.)
P60: Charge Distribution of Signal Peptides and Signal Anchor Type II, Masahiro
Gomi, Takatsugu Hirokawa, Shigeki Mitaku (Tokyo Univ. of Agriculture &Tech.)
P61: Topology Prediction of Membrane Proteins Based on a Modified “PositiveInside” Rule, Koji Kadota, Hiroyuki Sasamoto, Takatsugu Hirokawa, Shigeki
Mitaku (Tokyo Univ. of Agriculture & Tech.)P62: Classification of Membrane Proteins by Types of Transmembrane Helices Using
SOSUI System, Shigeki Mitaku, Takatsugu Hirokawa, Mitsuo Ono (Tokyo Univ.
of Agriculture & Tech.)P63: Gene Classification by Self-Organization Mapping of Codon Usage in Bacteria with Completely Sequenced Genome, Shigehiko Kanaya∗ , Yoshihiro Kudo∗ ,Takashi Abe∗ , Takanori Okazaki∗ , Carlos Del Carpio† , Toshimichi Ikemura‡(∗ Yamagata Univ., † Toyohashi Univ. of Tech., ‡ NIG)
P64: GAFLEX: A Hybrid GA Engine for Mapping the Configuration Hyper-Spaceof Organic Compounds in Solution, Carlos A. Del Carpio (Toyohashi Univ. of
Tech.)
P65: DYNAX: A New System for Biomolecular Dynamics Simulation in Solution,
Atsushi Yoshimori, Carlos A. Del Carpio (Toyohashi Univ. of Tech.)
P66: Development of an Antibacterial MAP Homologous to a Loop Region in Human
Lactoferrin, Masachika Azuma, Taiki Kojima, Masaki Kobayashi, Carlos Adriel
Del Carpio (Toyohashi Univ. of Tech.)
P67: MOLDEX:A Computer System for Drug Design. 4)A Combined Electro-Geometric
Method for the Identification of Pharmacophoric Structural Patterns in Drugs,
Hiromi Nakatake, Carlos Adriel Del Carpio (Toyohashi Univ. of Tech.)P68: A Simulated Annealing Algorithm for Geometrical Assessment of Macromolecular Hydrophobic Interaction, Tomoko Hara, Carlos Adriel Del Carpio (Toyohashi
Univ. of Tech.)P69: A Genetic Programming Based System for the Prediction of Secondary andTertiary Structures of RNA, Katsuhisa Yamaguchi, Carlos Adriel Del Carpio(Toyohashi Univ. of Tech.)P70: Detailed Sequence Analysis of the Distal Down Syndrome Critical Region and
the SOD1/AML1 Region on Chromosome 21, Todd Taylor∗ , Masahira Hattori∗ ,Kiyoteru Noguchi† , Tomomi Shobu∗ ,Kazuo Ishii∗ , Atsushi Toyoda∗ , Yoshiyuki
Sakaki∗ (∗ Univ. Tokyo, † Hitachi, Ltd.)P71: Genome Wide Survey of the Entire C. elegans alpha-Tubulin Gene Family:
cDNA Cloning, Expression, and Structure-Function Analysis, Camelia B. Gogonea∗ ,M. Y. Ali∗ , Tetsunari Fukushige† , M. Afaq Shakir‡ , Takashi Matsuo∗ , Shahid
S. Siddiqui∗ (∗ Toyohashi Univ. Tech., † Univ. Caigary, Canada, ‡ Mass. Gen.
Hosp., USA)
P72: Gene Has Its Inherent Significantly Repetitive Tuples, Nobuyuki Uchikoga,
Akira Suyama (Univ. Tokyo)
P73: Nucleotide Sequence of a Gene Encodes Characteristic Features of an Organism
as Well as an Amino Acid Sequence, Hiroshi Nakashima∗ , Motonori Ota† , Ken
Nishikawa† , Tatsuo Ooi‡ (∗ Kanazawa Univ., † NIG, ‡ Kyoto Women’s Univ.)
P74: Application Computer Software in Mapping Quantitative Trait Loci, Chindo
Hicks, Eiji Kobayashi, Masahiro Satoh, Kazuo Ishii, Tsutomu Furukawa (NIAI)
P75: Phosphoglycerate-transporter Protein B as a Most Primitive Protein Predictedby the Poly-tRNA Theory, Koji Ohnishi (Niigata Univ.)
P76: Sequence Analysis of the IRES-Loop III Region of Hepatitis C Virus, Takayoshi
Sasano, Jun-Ichi Sagara, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu(Univ. Tokyo)

P77: ORF Clustering Analysis of 17 Complete Genomes, Kenji Suzuki∗ , Takeshi Ara∗ ,Hideo Matsuda† , Hirotada Mori∗ (∗ AIST-NARA, † Osaka Univ.) [P77 is notincluded in the book because the final manuscript was not in time for publication
but included in CD-ROM.]

Commercial Exhibitions
C1: Nihon SiliconGraphics K.K.
C2: Ryoka Systems Inc.
C3: Mitsui Knowledge Industry Co., Ltd.
C4: Software Development Co., Ltd.
C5: CTC LABORATORY SYSTEMS CORP.
C6: Teijin Systems Technology Ltd.
C7: Hitachi, Ltd.
C8: Sumisho Electronics Co.
C9: Perkin-Elmer Japan Co., Ltd.
C10: Paracel Inc.

Location
The workshop will take place at the Garden Hall which is located in the Yebisu Garden
Place. Please get off at JR Ebisu Station or Ebisu Station on the Eidan Subway
Hibiya Line. It takes about 5 minutes walk from the east exit JR EBISU station to
Yebisu Garden Place if you use the “Yebisu Skywalk” covered moving walkway. The
address/TEL/FAX of Yebisu Garden Place are as follows:
1-13-2 Mita, Meguro-ku, Tokyo 153-0062, Japan
TEL: +81-3-5424-0111 FAX: +81-3-5424-1444
URL: http://www.sgi.co.jp/YGP/ (Japanese)Getting There
Tokyo is the capital city of Japan.There are direct flights to Narita International
Airport from many countries.You can take trains from the airport.
After arriving in Narita International Airport,take a train (either JR line or Keiseiline) from the airport station:
1. JR line:
Using Express (Narita Express) train,it takes about 1 hour from the airport
station to JR Tokyo station.From JR Tokyo station to JR Ebisu station,take
JR Yamanote line to the direction of Shinagawa and Shibuya.It takes about 30
minutes.
2. Keisei line:
Using Express (Skyliner) train,it takes about 1 hour from the airport station to
Keisei Ueno station.It takes about 5 minutes walk from Keisei Ueno station to
JR Ueno station.From JR Ueno station to JR Ebisu station,take JR Yamanoteline to the direction of Tokyo and Shinagawa. It takes about 40 minutes.
Go along the Sky Walk from the east exit of JR Ebisu station. After 5 minutes
walk, you will find the entrance to the Yebisu Garden Place.

Passport and Visa Requirements
All overseas visitors wishing to enter Japan require a valid Passport. Visa will also be
required for participants coming from the countries without visa exemption agreementswith Japan.
Entry into Japan for 90 days is very easy to obtain a Visa. Participants requiring
visas should apply well in advance to Japanese consular offices or diplomatic missions
in their countries prior to making final travel arrangements with a travel agent.
For more information about visa,please see
http://www.mofa.go.jp/visa(The Ministry of Foreign affairs,Japan)
If you require a letter advising your registration for the conference,please E-mail :giw@ims.u-tokyo.ac.jp.