Genome Informatics Vol. 3 (1992)

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Genome Informatics Vol. 3 (1992)

Presented at the Genome Informatics Workshop 1992
December 14-15, 1992, Yokohama, Japan

Published as: S. Mitaku, T. Takagi, M. Kanehisa, O. Gotoh, K. Nitta, M. Hagiya, A. Yonezawa, R. Kataoka(eds.) "Genome Informatics Workshop 1992"

 


 

Oral Session

 

Integration of Local Area Network system in Natioal Cancer Center, and study for network-aided genetic information analysis system
Hiroshi Mizushima, Yoshiyuki Kuchino
Genome Informatics 3: 21-24 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Building and Searching DNA Data Base on a Relational Model
Hajime Kitakami, Yukiko Yamazaki, Yoshio Ugawa, Kazuo Ikeo, Naruya Saitou, Yoshio Tateno, Takashi Gojobori
Genome Informatics 3: 25-28 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Compartmentalization of the Human Genome
Toshimichi Ikernura, Kimihiko Sugaya, Ken-nosuke Wada
Genome Informatics 3: 29-32 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Assessment of Lysogenisity of Temperate Phages: Comparison of Repressibility of Promoter-like Sequneces among Escherichia coli and its Phages (P4 andlambda)
Shigehiko Kanaya, Yoshihiro Kudo
Genome Informatics 3: 33-36 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Quantification Analysis of Translation Initiation Signal Sequences in Vertebrate mRNAs
Yoichi Iida
Genome Informatics 3: 37-40 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Evolution from Semi-tRNA to tRNAs, rRNAs, snRNA and Primitive mRNAs
Koji Ohnisi
Genome Informatics 3: 41-44 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

RNA Secondary Structure Prediction Using a Highly Parallel Computer
Yoshisato Takeda, Kenji Yamamoto, Masahiro Yasugi, Akinori Yonezawa
Genome Informatics 3: 45-48 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Does an Aberrant Splicing Database Imply Rules for Splice Site Selection?
Kenta Nakai, Yutaka Akiyama, Hiroshi Sakamoto
Genome Informatics 3: 49-52 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Algorithms for the Longest Common Subsequence Problem
Koji Hakata and Hiroshi Imai
Genome Informatics 3: 53-56 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Expressing a Set of Strings for Genome Information and DP Matching
Minoru Icchoda, Nobuo Takiguchi, Yoshiyuki Kotani
Genome Informatics 3: 57-60 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Sequence Analysis and Assembly Using the Fast Data Finder (TM) 3
Timothy Burcham, James Candlin, Alan Roter
Genome Informatics 3: 61-64 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Tiny Step toward Rule-based Protein Sequence Analysis System
Makoto Hirosawa, Masato Ishikawa, Masaki Hoshida
Genome Informatics 3: 65-68 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Knowledge Acquisition from Amino Acid Sequences by Decision Trees and Indexing
Satoru Miyano, Ayumi Shinohara, Setsuo Arikawa, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara
Genome Informatics 3: 69-72 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Trial to Determine Identity of Proteins by Motifs
Y. Seto, Y. Ikeuchi, S. Kawakita, K. Nishikawa, M. Kanehisa
Genome Informatics 3: 73-76 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Prediction of the Functional Sites in Amino Acid Sequences
Yukihiro Eguchi, Yasuhiko Seto
Genome Informatics 3: 77-80 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Recognition of Weak Homology of Proteins Using Information from 3D-structures
Yo Matsuo, Ken Nishikawa
Genome Informatics 3: 81-84 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Automatic Determination of Hydrophobic Cores
Mark B. Swindells
Genome Informatics 3: 85-888 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

An Exploration of Using a Modular Neural Network to Predict the Secondary Structures through a Variation in the Description of the Output States
Fumiyoshi Sasagawa, Koji Tajima
Genome Informatics 3: 89-92 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Protein aipha-Helix Region Prediction Using Stochastic-Rule Learning
Hiroshi Mamitsuka, Kenji Yamanishi
Genome Informatics 3: 93-96 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Continuous Speech Recognition Techniques for Protein Structure Prediction Systems
Kiyoshi Asai, Satoru Hayamizu, Kentaro Onizuka, Ken-ichi Handa
Genome Informatics 3: 97-100 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

An Algorithm for Extraction of Secondary Structure from Imperfect Protein Tertiary Structure Data
Yasuo Yonezawa
Genome Informatics 3: 101-104 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Similar Structure Search Function of PACADE for Analyzing Three Dimensional Structures of Protein
Kenji Satou, Satoru Kuhara, Emiko Furuichi, Kyoko Takiguchi, Toshihisa Takagi
Genome Informatics 3: 105-108 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Protein Tertiary Structure Search System
Seiichi Aikawa, Mayumi Tomikawa, Fumiko Matsuzawa
Genome Informatics 3: 109-112 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

The Classification of Local Structures for Modeling Protein Structure Geometric Constraints
Kentaro Onizuka, Kiyoshi Asai, Stephen T. C. Wong
Genome Informatics 3: 113-116 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Development of the Protein Tertiary Structure Prediction System III: Simulation of Folding Process of Lysozyme
Kouji Tabuchi, Tamio Yasukawa, Masaki Fumoto
Genome Informatics 3: 117-120 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Ordering and Mapping of Cosmid Clones under Semi-automated System
Eiichi Soeda, De-Xing Hou, Tetsusi Yamagata, Haruo Kishida, Takanori Shimokawa, Hiroshi Furuhashi, Emiko Soeda, Yasuo Atsuchi
Genome Informatics 3: 121-124 (1992)
[Abstract]  [Full-text HTML]   [Full-text PDF]

 

Poster Session

 

Data Analysis of Chromosome-Profiles
Yoshio Noguchi
Genome Informatics 3: 125-128 (1992)
[Abstract]   [Full-text PDF]

Physical Mapping of Commonly Deleted Region on Chromosome 3p in Human Cancers Based on Radiation Hybrid (RH) Mapping
Hirokuni Takano, Takashi Kohno, Hiroaki Shimizu, Ryuya Shimoda, Naohito Yamaguchi, Jun Yokota
Genome Informatics 3: 129-132 (1992)
[Abstract]   [Full-text PDF]

A Rapid Mapping System for Assigning Cosmid Clones to Human Chromosome 21 by Dot Analysis
De-Xing Hou, Toshitugu Okayama, Takurou Tamura, Eiichi Soeda
Genome Informatics 3: 133-137 (1992)
[Abstract]   [Full-text PDF]

Drawing Dot-matrix Similarity Plots with the Sequence Position Tree
Christophe Lefevre
Genome Informatics 3: 139-142 (1992)
[Abstract]   [Full-text PDF]

Integrated Characterization of Transcriptional Upstream Sequences by Statistical Consensus Patterns and Experimental Data
Wataru Fujibuchi, Minoru Kanehisa
Genome Informatics 3: 143-146 (1992)
[Abstract]   [Full-text PDF]

Evolutionary Origin for the Multiplicity of Escherichia coli Response-Regulator Proteins
Takashi Kunisawa
Genome Informatics 3: 147-150 (1992)
[Abstract]   [Full-text PDF]

Anonymous FTP Prepared by PRF on Genome Network
Y. Ikeuchi, M. Isoyama, Y. Seto
Genome Informatics 3: 151-154 (1992)
[Abstract]   [Full-text PDF]

Bio-Net; A Tool to Support Genome Researchers
Yoshinari Watanabe, Shuji Kaneko, Ichiro Sora, Hiroyuki Hayashi, Naohiro Hohashi, Kei Hosokawa, Shigeo Masaki
Genome Informatics 3: 155-158 (1992)
[Abstract]   [Full-text PDF]

Free Energy Calculation of Random Sequence of RNA
Kenji Yamamoto, EIji Arakawa, Hiroshi Yoshikura
Genome Informatics 3: 267-270 (1992)
[Abstract]   [Full-text PDF]

Higher Information Processing of Protein AMino Acid Sequence Data: Development of A Computer System for the Analysis of Environmental Features of Protein's Amino Acid Sequence
Motokazu Kamimura, Hiroaki Kato, Yoshimasa Takahashi
Genome Informatics 3: 159-161 (1992)
[Abstract]   [Full-text PDF]

A New Method for Finding Packing Patterns of Protein C alpha Segments
Zenmei Ohkubo, Minoru Kanehisa
Genome Informatics 3: 163-166 (1992)
[Abstract]   [Full-text PDF]

The Molecular Modeling of Membrane Protein by Enerrgy Calculation
Makiko Suwa, Shigeki Mitaku, Nobuhiko Saito
Genome Informatics 3: 167-170 (1992)
[Abstract]   [Full-text PDF]

Three Dimensional Structures and Molecular Evolutions of Proteins I. The Ongin of Serine Proteases
Takeshi Fukuhara, Haretsugu Hishigaki, Tamio Yasukawa
Genome Informatics 3: - (1992)
[Abstract]   [Full-text PDF]

Koichi Niijima, Takeshi Shinohara, Yoshihiro Mizoguchi, Shinichi Shimozono
Learning of Three-Layered Neural Networks by the Contraction Mapping Principle: Application to Genome Data Analysis
Genome Informatics 3: 175-178 (1992)
[Abstract]   [Full-text PDF]

Self-Operation Models and Self-Reproductive Strand
Yoshiteru Ishida
Genome Informatics 3: 179-182 (1992)
[Abstract]   [Full-text PDF]

The Distribution Profiles of GC Content Surrounding the Translation Initiation Site in Different Species
Masahiko Mizuno, Minoru Kanehisa
Genome Informatics 3: 183-186 (1992)
[Abstract]   [Full-text PDF]

Towards an Analysis of Mutants Spectra on the Sequence Space II
Yuzuru Husimi, Makoto Marutani
Genome Informatics 3: 187-190 (1992)
[Abstract]   [Full-text PDF]

 

Workstation Session

 

Introduction to the GenomeNet
Atsushi Ogiwara, Ikuo Uchiyama, Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 3: 191-194 (1992)
[Abstract]   [Full-text PDF]

Genomatica: An Integrated Management Tool for Genome Sequencing Projects
Yutaka Akiyama, Hirotada Mori, Satoru Kuhara, Tetsuya Furukawa, Kenji Satou, Nobuyuki Miyajima, Naoki Ogasawara, Yasufumi Murakami
Genome Informatics 3: 195-198 (1992)
[Abstract]   [Full-text PDF]

NeuroFold: An RNA Secondary Structure Prediction System Using a Hopfield Neural Network
Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 3: 199-202 (1992)
[Abstract]   [Full-text PDF]

Construction and Application of a Relational Dattbase That Links Amimo Acid Sequence Motifs to Chemical Compounds
Mikita Suyama, Atsushi Ogiwara, Takaaki Nishioka and Jun'ichi Oda
Genome Informatics 3: 203-206 (1992)
[Abstract]   [Full-text PDF]

A Computer System for Predicting Membrane Protein Structure
Takatsugu Hirokawa, Takaharu Saito, Nobuhiro Kimura, Makiko Suwa, Shigeki Mitaku
Genome Informatics 3: 207-210 (1992)
[Abstract]   [Full-text PDF]

G Shell (gsh): Flexible and Extensible Environment for Genome Information Analysis
Akira Suyama, Hiroaki Kaku
Genome Informatics 3: 211-214 (1992)
[Abstract]   [Full-text PDF]

Emacs Interface for Sybase
Masami Hagiya
Genome Informatics 3: - (1992)
[Abstract]   [Full-text PDF]

GeneView: A Human Genome Mapping Library System on the Workstation
Shinsei Minoshima, Hiroshi Hohi, Mitsuru Ishizuka, and Nobuyoshi Shimizu
Genome Informatics 3: 215-218 (1992)
[Abstract]   [Full-text PDF]

HyperGenome: An Integrated System for Mapping Data
Satoru Kuhara, Toshihisa Takagi, Minoru Kanehisa
Genome Informatics 3: 219-222 (1992)
[Abstract]   [Full-text PDF]

Object-Oriented Database with Logical Query Interface for Genomic Computation
Susumu Goto, Norihiro Sakamoto, Toshihisa Takagi
Genome Informatics 3: 223-226 (1992)
[Abstract]   [Full-text PDF]

Network Servers of DNA Data Bank of Japan (DDBJ)
Yoshihiro Ugawa, Hajime Kitakami, Yukiko Yamazaki, Kazuho Ikeo, Mari Saito, Masashi Uchino, Toshiya Sakamaki, Shigeru Kanemoto, Nobuyuki Fujita, Masataka Takekoshi, Shuji Kaneko, Hideya Yoshida, Hiro Amano, Yasuo Ina, Naruya Saito, Takashi Gojobori, Yoshio Tateno
Genome Informatics 3: 227-230 (1992)
[Abstract]   [Full-text PDF]

Human Genome Mapping Database for Macintosh
Asao Fujiyama
Genome Informatics 3: 231-234 (1992)
[Abstract]   [Full-text PDF]

Demonstration of GDB: GDB (Genome Data Base) The International Human Genome Data Base
Masahiko Suzuki, Mika Hirakawa
Genome Informatics 3: 235-238 (1992)
[Abstract]   [Full-text PDF]

Guidance of Access to Bio-Net Hosted on the NIFTY-Serve Network and Demonstration of On-line Softwares to Aid a Genome Research
Naohiro Hohashi, Shuji Kaneko, Ichiro Sora, Hiroyuki Hayashi, Kei Hosokawa, Shigeo Masaki, Yoshinari Watanabe
Genome Informatics 3: 239-242 (1992)
[Abstract]   [Full-text PDF]

Motif Database Handling System BIORESEACH/PR
Tatsuya Shiobara, Kosei Shimokomaki, Chinatsu Nakanishi
Genome Informatics 3: 243-246 (1992)
[Abstract]   [Full-text PDF]

Sequence Analysis of Human Genome: Prediction of Protein Coding Region in DNA Sequences
Kotoko Nakata, Toru Yoshino, Yasushi Kubota, Akinori Sarai
Genome Informatics 3: 247-250 (1992)
[Abstract]   [Full-text PDF]

Speed-up of Information Retrieval by Data Compression
Takeshi Shinohara, Shuichi Fukumachi
Genome Informatics 3: 251-254 (1992)
[Abstract]   [Full-text PDF]

BONSAI: Knowlege Acquisition System by Decision Trees over Regular Patterns
Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara
Genome Informatics 3: 255-258 (1992)
[Abstract]   [Full-text PDF]

A Protein Sequence Alignment Editor based on KANAE
Koichi Yamagishi, Michiyo Yano, Akihiko Konagaya
Genome Informatics 3: 259-262 (1992)
[Abstract]   [Full-text PDF]

Protein Sequence Alignment by Parallel Iterative Method
Masato Ishikawa, Masaki Hoshida, Makoto Hirosawa, Tomoyuki Toya, Yasushi Totoki
Genome Informatics 3: 263-266 (1992)
[Abstract]   [Full-text PDF]

 

Invited Lectures

 

'Massively' Parallel Computing and Genome Information Processing
Akinori Yonezawa

Medical Application of the Human Genome Project
Yusuke Nakamura

New Databases and Software Tools for Molecular Biology at the National Center for Biotechnology Information
Jim Ostell

Algorithmic Learning Theory and Motif Discovery
Setsuo Arikawa