Genome Informatics Vol. 5 (1994)

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Genome Informatics Vol. 5 (1994)

Presented at the Genome Informatics Workshop 1994
December 19-20, 1994, Yokohama, Japan

Published as: S. Miyano, T. Akutsu, H. Imai, O. Gotoh and T. Takagi (eds.) "Genome Informatics Workshop 1994"
Universal Academy Press, Inc., Tokyo, 1994

Preface by Satoru Miyano

 


 

Oral Session

 

New Hashing Techniques for Three-Dimensional Protein Structures
Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa
Genome Informatics 5: 1-10 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Prediction of protein structural similarities using a 3D-1D compatibility method
Yo Matsuo, Ken Nishikawa
Genome Informatics 5: 11-18 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Prediction of Beta-Sheet Structures Using Stochastic Tree Grammars
Hiroshi Mamitsuka, Naoki Abe
Genome Informatics 5: 19-28 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Modeling RNA Secondary Structures Using Tree Grammars
Satoshi Kobayashi, Takashi Yokomori
Genome Informatics 5: 29-38 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Protein Motif Discovery from Positive Examples by Minimal Multiple Generalization over Regular Patterns
Hiroki Arimura, Ryoichi Fujino, Takeshi Shinohara, Setsuo Arikawa
Genome Informatics 5: 39-48 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Indexing protein sequences with MINOS
Huques Ropoche, Engelbert Mephu Nguifo, Jean Sallantin
Genome Informatics 5: 49-48 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Comparative Analysis of Amino Acid Sequences based on Rough Sets and Domain Knowledge Hierarchy
Shusaku Tsumoto, Hiroshi Tanaka, Kohei Tsumoto, Izumi Kumagai
Genome Informatics 5: 59-69 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Simulative representation of biological knowledge using object-oriented database language
Makoto Hirosawa, Reiko Tanaka, Hidetoshi Tanaka, Masayuki Akahoshi, Masato Ichikawa
Genome Informatics 5: 70-79 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

GEISHA SYSTEM: An Environment for Simulating Protein Interaction
Masanori Arita, Masami Hagiya, Tomoki Shiratori
Genome Informatics 5: 80-89 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Fast A* Algorithms for Multiple Sequence Alignment
Takahiro Ikeda, Hiroshi Imai
Genome Informatics 5: 90-99 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Multiple sequence alignment using anchor points through generalized dynamic programming
Jerome Gracy, Jean Sallantin
Genome Informatics 5: 100-109 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Multiple RNA-Sequence Alignment Considering Stem Regions
Masato Ishikawa, Tomoyuki Toya, Yasushi Totoki, Reiko Tanaka
Genome Informatics 5: 110-119 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data and Its Parallelization
Hideo Matsuda, Hiroshi Yamashita, Yukio Kaneda
Genome Informatics 5: 120-129 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Distribution of Base Composition around the Splice Sites in Different Species
Masahiko Mizuno, Minoru Kanehisa
Genome Informatics 5: 130-137 (1994)
[Abstract]  [Full-text HTML]   [Full-text PDF]

 

Poster Session

 

Construction and analysis of Escherichia coli genome database
Takeshi Itoh, Minoru Yano, Keiko Takemoto, Yutaka Akiyama, Hirotada Mori
Genome Informatics 5: 138-139 (1994)
[Abstract]   [Full-text PDF]

YAYOI: large Taxonomy Database System over International Computer Networks
Hajime Kitakami, Yoshio Tateno, Takashi Gojobori
Genome Informatics 5: 140-141 (1994)
[Abstract]   [Full-text PDF]

Establishment of Transcription Factor Database and Human Mutation Database
Hiroshi Mizushima, Kenshi Hayashi
Genome Informatics 5: 142-143 (1994)
[Abstract]   [Full-text PDF]

A Signal Transduction Database
Kenji Suzuki, Susumu Goto, Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 5: 144-145 (1994)
[Abstract]   [Full-text PDF]

The Gene Network: Development of a Database System Showing the Relationships Among the Genes of All Species
Nobuyuki Miyajima, Shinobu Nakayama, Mitsuyo Kohara, Satoko Hayashi
Genome Informatics 5: 146-147 (1994)
[Abstract]   [Full-text PDF]

Construction of a Membrane Protein Database and an Evaluation of Several Prediction Methods of Transmembrane Segments
Toshio Shimizu, Kenta Nakai
Genome Informatics 5: 148-149 (1994)
[Abstract]   [Full-text PDF]

The Prediction of Lateral and Rotational Positioning of α-Helices in a Membrane Protein
Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku
Genome Informatics 5: 150-151 (1994)
[Abstract]   [Full-text PDF]

Protein Three Dimensional Structure Prediction on Object Oriented Database
Akira Shimada, Hideki Takehara, Kazunori Toma
Genome Informatics 5: 152-153 (1994)
[Abstract]   [Full-text PDF]

Computing Closures of Indirect Similarity Relationships among Structures in Proteins
Kenji Satou, Emiko Furuichi, Shin'ichi Hashimoto, Yukiko Tsukamoto, Satoru Kuhara, Toshihisa Takagi, Kazuo Ushijima
Genome Informatics 5: 154-155 (1994)
[Abstract]   [Full-text PDF]

Automatic Labeling of Protein Structures by Hidden Markov Models
Kiyoshi Asai, Kentaro Onizuka, Masayuki Akahoshi, Hidetoshi Tanaka, Katunobu Itou
Genome Informatics 5: 156-157 (1994)
[Abstract]   [Full-text PDF]

A New Method for Predicting Long-range Interactions between Amino Acid Residues Based-on Homological Correlations
Hiroshi Mamitsuka
Genome Informatics 5: 158-159 (1994)
[Abstract]   [Full-text PDF]

Reverse Evolution of Proteases Studied by a Modified 3D-1D Method
Haretsugu Hishigaki, Tamio Yasukawa
Genome Informatics 5: 160-161 (1994)
[Abstract]   [Full-text PDF]

An Approach to Three-Dimensional Motif Finding in Proteins
Hiroaki Kato, Yoshimasa Takahashi
Genome Informatics 5: 162-163 (1994)
[Abstract]   [Full-text PDF]

Discriminative Analysis of the Conformational Patterns of Protein Amino Acid Residues
Motokazu Kamimura, Yoshimasa Takahashi
Genome Informatics 5: 164-165 (1994)
[Abstract]   [Full-text PDF]

Protein Secondary Structure Analysis Using Neural Network
Kotoko Nakata
Genome Informatics 5: 166-167 (1994)
[Abstract]   [Full-text PDF]

Finding Functional Features of Proteins using Machine Learning Techniques
Takashi Ishikawa, Shigeki Mitaku, Takako Terano, Takatsugu Hirokawa, Makiko Suwa, Seah Boon Chieng
Genome Informatics 5: 168-169 (1994)
[Abstract]   [Full-text PDF]

Assignment of Certainty-Factor Parameters with a Given Reasoning Tree for the Prediction of Protein Localization Sites
Kenta Nakai, Ayumi Shinohara, Satoru Miyano
Genome Informatics 5: 170-171 (1994)
[Abstract]   [Full-text PDF]

Discrimination of intracellular and extracellular proteins by single residue and residue-pair scores
Hiroshi Nakashima, Ken Nishikawa
Genome Informatics 5: 172-173 (1994)
[Abstract]   [Full-text PDF]

Classification of Possible Proteins from Genome Sequencing
Yukihiro Eguchi, Yuzo Ueda
Genome Informatics 5: 174-175 (1994)
[Abstract]   [Full-text PDF]

Alphabet Indexing by Cluster Analysis: A Method for Knowledge Acquisition from Amino Acid Sequences
Hideaki Nakakuni, Takeo Okazaki, Satoru Miyano
Genome Informatics 5: 176-177 (1994)
[Abstract]   [Full-text PDF]

DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm
Tetsushi Yada, Masato Ishikawa, Hidetoshi Tanaka, Kiyoshi Asai
Genome Informatics 5: 178-179 (1994)
[Abstract]   [Full-text PDF]

Detecting common amino acid sequence patterns with a gap
Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda
Genome Informatics 5: 180-181 (1994)
[Abstract]   [Full-text PDF]

Multiple Sequence Alignment with a Tree-Based Weighting System
Osamu Gotoh
Genome Informatics 5: 182-183 (1994)
[Abstract]   [Full-text PDF]

Integration of Minimum Evolution and Maximum Likelihood Method in Constructing Molecular Evolutionary Tree
Hiroshi Tanaka, Fengrong Ren, Norio Fukuda
Genome Informatics 5: 184-185 (1994)
[Abstract]   [Full-text PDF]

Relationship between Gene Function and Codon Usage in Escherichia coli on the basis of Principal Component Analysis
Shigehiko Kanaya, Toshimichi Ikemura, Yoshihiro Kudo
Genome Informatics 5: 186-187 (1994)
[Abstract]   [Full-text PDF]

Estimation of protein-production levels for ORFs found by E. coli and yeast genome projects, basing on levels of ``optimal codon'' usage, in connection with feasibility of their protein coding ability and with assignment to foreign-type genes.
Yasukazu Nakamura, Tatsuo Fukagawa, Kimihiko Sugaya, Toshimichi Ikemura
Genome Informatics 5: 188-189 (1994)
[Abstract]   [Full-text PDF]

A Set of Tools Developed for the Analysis of Open Reading Frames of Yeast (S.cerevisiae) Chromosome VI
Motoe Sasanuma, Zhong-qing Wang, Kazuhiro Shibata, Syun-ichi Sasanuma, Masashi Ozawa, Eiko Kohriki, Toshihiko Eki, Akinori Sarai, Hideaki Sugawara, Yasufumi Murakami
Genome Informatics 5: 190-191 (1994)
[Abstract]   [Full-text PDF]

Evaluation of the Sequence Data Assemble Software "Shotgun"
Zhong-qing Wang, Yasufumi Murakami, Toshihiko Eki, Akira Oyama, Yukihiro Eguchi, Akinori Sarai, Hideaki Sugawara
Genome Informatics 5: 192-193 (1994)
[Abstract]   [Full-text PDF]

Rapid identity searching program for DNA sequences and its applications to cDNA grouping
Tetsuo Nishikawa, Susumu Hiraoka, Naoko Kasahara, Keiichi Nagai
Genome Informatics 5: 194-195 (1994)
[Abstract]   [Full-text PDF]

 

Workstation Session

 

Locus-in v.2 and GeneView PLUS : Computer softwares for entry and analysis of the human genome data
Shinsei Minoshima, Nobuyoshi Shimizu
Genome Informatics 5: 196-197 (1994)
[Abstract]   [Full-text PDF]

ContigMaker and SAND: Software Tools for Genome Mapping and Sequencing
Akira Suyama, Akira Ohyama, Masami Hagiya, Yoshiaki Furuhata, Takashi Ito, Asao Fujiyama, Masahira Hattori, Yoshiyuki Sakaki, Toshishisa Takagi
Genome Informatics 5: 198-199 (1994)
[Abstract]   [Full-text PDF]

Gnome: Recent Developments
Toshiyuki Niiyama, Atsushi Takeuchi, Kouichi Kotani, Ikuo Uchiyama, Atsushi Ogiwara, Kenta Nakai
Genome Informatics 5: 200-201 (1994)
[Abstract]   [Full-text PDF]

A server-client version of ''Genomatica'' integrated genome information browser
Yutaka Akiyama, Takahiro Yokoh, Hirotada Mori, Naotake Ogasawara
Genome Informatics 5: 202-203 (1994)
[Abstract]   [Full-text PDF]

Extension of the Integrated Database ''HyperGenome'' for Genome Maps and Sequence Information

Genome Informatics 5: 204-205 (1994)
[Abstract]   [Full-text PDF]

Further Improvements on SMART: Sequence Motif Analysis and Retrieval Tool
Atsushi Ogiwara, Ikuo Uchiyama, Toshihisa Takagi, Minoru Kanehisa
Genome Informatics 5: 206-207 (1994)
[Abstract]   [Full-text PDF]

Gidre : Genome Integrated Databases Retrieval Environment
Kagehiko Kitano, Atsushi Ogiwara, Toshihisa Takagi
Genome Informatics 5: 208-209 (1994)
[Abstract]   [Full-text PDF]

GenomeCruiser: A Laboratory Notebook for Human Gene Mapping
Hiroshi Dohi, Hideaki Sugawara
Genome Informatics 5: 210-211 (1994)
[Abstract]   [Full-text PDF]

A DNA Sequencing Project Monitoring and Sequence Data Quality Control System
Akira Ohyama, Masaki Takazawa, Atsuko Kubota, Nobuyuki Miyajima
Genome Informatics 5: 212-213 (1994)
[Abstract]   [Full-text PDF]

Animal Genome Database for Network Users
Yasuhiko Wada, Kengo Inoue, Hiroshi Yasue
Genome Informatics 5: 214-215 (1994)
[Abstract]   [Full-text PDF]

Menu System Based on NCSA Mosaic and Programs Forked from the Menu
Teruo Yasunaga, Tatsuya Takagi, Takeo Tokimori, Kouichi Kotani, Atsushi Takeuchi, Toshiyuki Niijima
Genome Informatics 5: 216-217 (1994)
[Abstract]   [Full-text PDF]

An Attempt to Integrate Various Protein Databases Using an Object-Oriented Database Management System
Hiromi Suzuki, Hiroaki Katoh
Genome Informatics 5: 218-219 (1994)
[Abstract]   [Full-text PDF]

A DNA/protein sequence retrieval system: an Xtpanel application
Akihiro Oda, Jun-ichi Yano, Minoru Kanehisa
Genome Informatics 5: 220-221 (1994)
[Abstract]   [Full-text PDF]

Rapid similarity search algorithm of nucleic acid database
Susumu Hiraoka, Keiichi Nagai
Genome Informatics 5: 222-223 (1994)
[Abstract]   [Full-text PDF]

Enhancement of the ''PROTEIX'' Database System for Three-Dimensional Protein Structures
Tatsuya Akutsu, Toshio Hyakutake
Genome Informatics 5: 224-225 (1994)
[Abstract]   [Full-text PDF]

A computer system for predicting membrane protein structure
Takatsugu Hirokawa, Seah Boon Chieng, Makiko Suwa, Shigeki Mitaku
Genome Informatics 5: 226-227 (1994)
[Abstract]   [Full-text PDF]

BONSAI Garden: Parallel Machine Discovery System for Sequences
Takayoshi Shoudai, Tomoyuki Uchida, Satoru Miyano, Ayumi Shinohara, Shinichi Shimozono, Takeo Okazaki, Takeshi Shinohara, Satoru Kuhara, Setsuo Arikawa
Genome Informatics 5: 228-229 (1994)
[Abstract]   [Full-text PDF]

SIMFLY: The Simulation of a Fly Embryo
Masanori Arita, Masami Hagiya, Tomoki Shiratori
Genome Informatics 5: 230-231 (1994)
[Abstract]   [Full-text PDF]

A Knowledge Base of Biological Cascades
Hidetoshi Tanaka, Makoto Hirosawa, Reiko Tanaka, Masayuki Akahoshi, Masato Ishikawa
Genome Informatics 5: 232-233 (1994)
[Abstract]   [Full-text PDF]

A Knowledge Base for Searching and Browsing Metabolic Pathways
Susumu Goto, Minoru Kanehisa
Genome Informatics 5: 234-235 (1994)
[Abstract]   [Full-text PDF]

 

Invited Lectures

 

Application of the genome topographer system¥¥ to the study of complex human disease.
Thomas G. Marr
Genome Informatics 5: 236-237 (1994)
[Abstract]   [Full-text PDF]

Protein sequence databases in the context of genome projects
Amos Bairoch
Genome Informatics 5: 238-239 (1994)
[Abstract]   [Full-text PDF]

An Integrated Database of Biological Sequences, Scientific Literature, and 3-Dimensional Structure
Stephen H. Bryant
Genome Informatics 5: 240-241 (1994)
[Abstract]   [Full-text PDF]