Genome Informatics Vol. 4 (1993)

Presented at the Genome Informatics Workshop 1993
December 13-15, 1993, Yokohama, Japan

Published as: T. Takagi, H. Imai, S. Miyano, S. Mitaku, M. Kanehisa(eds.) "Genome Informatics Workshop 1993"
Universal Academy Press, Inc., Tokyo, 1993

Preface by Minoru Kanehisa


Oral Session

On Pattern Matching Methods for Three Dimensional Protein Structures
Tatsuya Akutsu
Genome Informatics 4: 1-9 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Motif Knowledge Base Based on Deductive Object-Oriented Database Language
Makoto Hirosawa, Reiko Tanaka, Masato Ishikawa
Genome Informatics 4: 10-16 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language
Hideo Matsuda
Genome Informatics 4: 17-24 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Searches for Topologically and Three Dimensionally Similar Structures in Proteins
Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi
Genome Informatics 4: 25-35 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Stochastic Context-Free Grammars in Computational Biology: Applications to Modeling RNA

Genome Informatics 4: 36-45 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Representing Inter-residue Dependencies in Protein Sequences with Probabilistic Networks
Hiroshi Mamitsuka
Genome Informatics 4: 46-55 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Protein Motif Extraction Using Hidden Markov Model
Yukiko Fujiwara, Akihiko Konagaya
Genome Informatics 4: 56-64 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Deductive Method for Construction and Visualization of Contigs in the STS Strategy
Masami Hagiya
Genome Informatics 4: 65-73 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Running Learning Systems in Parallel for Machine Discovery from Sequences
Ayumi Shinohara, Shinichi Shimozono, Tomoyuki Uchida, Satoru Miyano, Satoru Kuhara, Setsuo Arikawa
Genome Informatics 4: 74-83 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Parallel Iterative Aligner with Genetic Algorithm
Masato Ishikawa, Tomoyuki Toya, Yasushi Totoki, Akihiko Konagaya
Genome Informatics 4: 84-93 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Application of Parallelized DP and A* Algorithm to Multiple Sequence Alignment
Shiho Araki, Masahiro Goshima, Shin-ichiro Mori, Hiroshi Nakashima, Shinji Tomita, Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 4: 94-102 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Parallel Multiple Alignments and Their Implementation on CM5
Naoto Ukiyama, Hiroshi Imai
Genome Informatics 4: 103-108 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Extraction of Conserved or Variable Regions from a Multiple Sequence Alignment
Osamu Gotoh
Genome Informatics 4: 109-113 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Automatic extraction of motif candidates by pairwise sequence alignment.
Yasuhiko Seto, Yoshinori Ikeuchi, Masaharu Isoyama
Genome Informatics 4: 114-119 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Finding Κ-best Alignments of Multiple Sequences
Gen Shibayama, Hiroshi Imai
Genome Informatics 4: 120-129 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Are the Hidden Markov Models Promising in Protein Research ?
Kiyoshi Asai, Hidetoshi Tanaka, Katunobu Itou, Kentaro Onizuka
Genome Informatics 4: 130-139 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Protein 3D Structure Prediction Based on Multi-Level Description
Kentaro Onizuka, Kiyoshi Asai, Masato Ishikawa
Genome Informatics 4: 140-151 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Prediction of Structure of Globular Proteins II. Tertiary Structure
Nobihiko Saito, Motonori Ota
Genome Informatics 4: 152-156 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Theoretical Method for the Determination of Helix Configuration in Membrane Proteins
Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku
Genome Informatics 4: 157-166 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Method for Extracting Spatially Close Peptide Segments in Proteins
Zenmei Ohkubo, Minoru Kanehisa
Genome Informatics 4: 167-174 (1993)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Poster Session

Quantification Analysis of Translation Initiation Signal Sequences in Vertebrate mRNAs
Yoichi IIDA, Takeshi MASUDA
Genome Informatics 4: 175-182 (1993)
[Abstract]   [Full-text PDF]

Multiple Sequence Alignment using Parallel Genetic Algorithms
Koji Tajima
Genome Informatics 4: 183-187 (1993)
[Abstract]   [Full-text PDF]

Prediction of Protein Conformations by a Spin Glass Model (I)
Tsuyoshi Yoshizawa, Masaki Fumoto, Tamio Yasukawa
Genome Informatics 4: 188-196 (1993)
[Abstract]   [Full-text PDF]

Toward prediction of multi-states secondary structures of protein by neural network
Fumiyoshi Sasagawa, Koji Tajima
Genome Informatics 4: 197-204 (1993)
[Abstract]   [Full-text PDF]

Sequence Analysis of Zinc Finger DNA-Binding Protein
Kotoko Nakata
Genome Informatics 4: 205-210 (1993)
[Abstract]   [Full-text PDF]

Protein Sequence Motif Extraction with a Probabilistic Logic Neural Network: Motif Evaluation on a 3-D Structure

Genome Informatics 4: 211-218 (1993)
[Abstract]   [Full-text PDF]

Learning Algorithms of Three Layered Neural Networks for Sequence Classification
Koichi Niijima, Shinichi Shimozono
Genome Informatics 4: 219-223 (1993)
[Abstract]   [Full-text PDF]

Classification of Proteins via Successive State Splitting Algorithm of Hidden Markov Network
Hidetoshi Tanaka, Kentaro Oniduka, Kiyoshi Asai
Genome Informatics 4: 224-230 (1993)
[Abstract]   [Full-text PDF]

Assessment of Species-specific Codon Usage by Principal Component Analysis
Shigehiko Kanaya, Yoshihiro Kudo
Genome Informatics 4: 231-238 (1993)
[Abstract]   [Full-text PDF]

A search for CpG islands associated with genes in human genomic sequences compiled in the DNA database
Jun Kusuda, Makoto Hirata, Atushi Toyoda, Ichiro Takahashi, Katsuyuki Hashimoto
Genome Informatics 4: 239-244 (1993)
[Abstract]   [Full-text PDF]

Extraction of the ligand-related motifs in enzymes
Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda
Genome Informatics 4: 245-254 (1993)
[Abstract]   [Full-text PDF]

Automatic Procedure to Extract Signature Pentapeptides from the Protein Sequence Database
Ikuo Uchiyama, Atsushi Ogiwara, Zenmei Ohkubo, Minoru Kanehisa
Genome Informatics 4: 255-263 (1993)
[Abstract]   [Full-text PDF]

A Simple Method for Finding Local Sequence Similarities
Keiichi Nagai, Tetsuo Nishikawa, Hideki Kambara, Toshihisa Takagi
Genome Informatics 4: 264-269 (1993)
[Abstract]   [Full-text PDF]

A Computer Modeling Method for the Three-dimensional Structure of RNA
Hiroyuki Ogata, Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 4: 270-274 (1993)
[Abstract]   [Full-text PDF]

Construction of a Functional Word Dictionary for Primate Promoter Sequences
Watru Fujibuchi, Minoru Kanehisa
Genome Informatics 4: 275-282 (1993)
[Abstract]   [Full-text PDF]

A Similarity Measure for DNA Sequence Analysis Based on Locality
Takashi Yokomori, Satoshi Kobayashi
Genome Informatics 4: 283-292 (1993)
[Abstract]   [Full-text PDF]

Prediction of Structures of Globular Proteins I. Secondary Structure
Yukio Kobayashi, Nobuhiko Saito
Genome Informatics 4: 293-299 (1993)
[Abstract]   [Full-text PDF]

Variation of the Order of Importance in the Base Position for 5'-Splice Site Sequences
Khawaja Sirajuddin, Tomomasa Nagashima, Koichi Ono
Genome Informatics 4: 300-305 (1993)
[Abstract]   [Full-text PDF]

Analysis of Abnormal Splicing by Neural Network
Hiroshi Furutani
Genome Informatics 4: 306-314 (1993)
[Abstract]   [Full-text PDF]

Backbone Conformational Pattern Clustering of Three-Dimensional Peptide Fragments of Proteins
Motokazu Kamimura, Yoshimasa Takahashi
Genome Informatics 4: 315-324 (1993)
[Abstract]   [Full-text PDF]

Poly-tRNA Theory on the Origin and Evolution of mRNA and Genetic Codes: Evolution from Tandem tRNA-Repeats to Primitive mRNAs Encoding F0-ATPase a Subunit and Glycyl-tRNA Synthetase
Koji Onishi
Genome Informatics 4: 325-331 (1993)
[Abstract]   [Full-text PDF]

Metrics for Protein Sequence Comparison
Tsukasa Sakai
Genome Informatics 4: 332-338 (1993)
[Abstract]   [Full-text PDF]

Using Analogical Reasoning to Predict a Protein Structure
Takashi Ishikawa, Takao Terano
Genome Informatics 4: 339-346 (1993)
[Abstract]   [Full-text PDF]

A sensitive and efficient homology search method to find proteincoding regions using ''protein-coding region DNA database''
K. Wada, Y. Wada, S. Tanaka, H. Doi. Y. Nakamura, K. Sugaya, T. Fukagawa, T. Ikemura
Genome Informatics 4: 347-351 (1993)
[Abstract]   [Full-text PDF]

Workstation Session

Integration of Genome Databases Using a Deductive Object-Oriented Database
Susumu Goto, Norihiro Sakamoto, Toshihisa Takagi
Genome Informatics 4: 352-361 (1993)
[Abstract]   [Full-text PDF]

Enhancement of the Integrated Database "HyperGenome" for Genome Maps and Sequence Information
Takahiro Suzuki, Susumu Nakashima, Toshihisa Takagi, Satoru Kuhara, Minoru Kanehisa
Genome Informatics 4: 362-369 (1993)
[Abstract]   [Full-text PDF]

Locus-in: a new database system with graphical front end to integrate mapping data
Shinsei Minoshima, Nobuyoshi Shimizu
Genome Informatics 4: 370-375 (1993)
[Abstract]   [Full-text PDF]

ContigMaker: Software Tool for Contig Map Construction
Akira Suyama, Masami Hagiya, Takashi Ito, Asao Fujiyama, Akira Ohyama, Toshihisa Takagi
Genome Informatics 4: 376-384 (1993)
[Abstract]   [Full-text PDF]

GNOME: a sequence data management tool to access homology, motif, and other data analysis servers
Toshiyuki Niiyama, Takeo Tokimori, Atsushi Ogiwara, Ikuo Uchiyama, Kenta Nakai
Genome Informatics 4: 385-393 (1993)
[Abstract]   [Full-text PDF]

Genomatica: an integrated data management and analysis tool for genome sequencing projects
Yutaka Akiyama, Hirotada Mori, Satoru Kuhara, Naoki Ogasawara, Nobuyuki Miyajima, Tetsuya Furukawa, Kenji Sato, Yasufumi Murakami
Genome Informatics 4: 394-401 (1993)
[Abstract]   [Full-text PDF]

Sequence Motif Analysis and Retrieval Tool
Atsushi Ogiwara, Ikuo Uchiyama, Minoru Kanehisa
Genome Informatics 4: 402-410 (1993)
[Abstract]   [Full-text PDF]

Constraint Based Alignment Editor with Automatic Alinger and Motif Dictionary Retriever
Makoto Hirosawa, Yasushi Totoki, Masato Ishikawa
Genome Informatics 4: 411-417 (1993)
[Abstract]   [Full-text PDF]

A Three-Dimensional Graphic System for Protein Structure Analysis
Masayuki Akahoshi, Kentaro Onizuka, Masato Ishikawa, Kiyoshi Asai
Genome Informatics 4: 418-429 (1993)
[Abstract]   [Full-text PDF]

PROTEIX: An Interactive Database System for Three Dimensional Protein Structures
Tatsuya Akutsu
Genome Informatics 4: 430-433 (1993)
[Abstract]   [Full-text PDF]

A computer system for predicting membrane protein structure
Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku
Genome Informatics 4: 434-440 (1993)
[Abstract]   [Full-text PDF]

Knowledge library of proteins on anonymous FTP/genome network
Yoshinori Ikeuchi, Masaharu Isoyama, Yasuhiko Seto
Genome Informatics 4: 441-445 (1993)
[Abstract]   [Full-text PDF]

Development of a genetic information system for institute engaged in molecular biology
Hiroshi Mizushima, Yoshiyuki Kuchino
Genome Informatics 4: 446-450 (1993)
[Abstract]   [Full-text PDF]

Human Gene Database for a Personal Computer with Graphical Interface
Asao Fujiyama
Genome Informatics 4: 451-454 (1993)
[Abstract]   [Full-text PDF]

Invited Lectures

The ACEOB genome database: support for large scale sequencing projects
Richard Durbin
Genome Informatics 4: 455 (1993)
[Abstract]   [Full-text PDF]

Towards an information managemenet system for genomic objects and processes
Otto Ritter
Genome Informatics 4: 456 (1993)
[Abstract]   [Full-text PDF]

The Transformation of GDB
Robert J. Robbins
Genome Informatics 4: 457-458 (1993)
[Abstract]   [Full-text PDF]

Scoring Syatems for Macromolecular Sequence Comparison
Stephen F. Altschul
Genome Informatics 4: 459 (1993)
[Abstract]   [Full-text PDF]

Algorithmic Research Problems in Molecular Bioinformatics
Thomas Lengauer
Genome Informatics 4: 460 (1993)
[Abstract]   [Full-text PDF]

Super Parallel Computing Project: Scientific Research on Priority Areas for Ministry of Education
Hidehiko Tanaka
Genome Informatics 4: 461 (1993)
[Abstract]   [Full-text PDF]

Eukaryotic Gene Identification Algorithms
James W. Fickett
Genome Informatics 4: 462 (1993)
[Abstract]   [Full-text PDF]

Genome Sequence Analysis: Identifying and Classifying Genes
Phil Green
Genome Informatics 4: 463 (1993)
[Abstract]   [Full-text PDF]