Genome Informatics Vol. 8 (1997)

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Genome Informatics Vol. 8 (1997)

Presented at the Genome Informatics Workshop 1997
December 12-13, 1997, Yebisu Garden Place, Tokyo, Japan

Published as: Miyano, S. and Takagi, T. (eds.) "Genome Informatics 1997"
Universal Academy Press, Tokyo, 1997

Preface by Satoru Miyano

 

 


 

Full Talk Papers

 

Automatic Gene Recognition without Using Training Data
Kiyoshi Asai, Yutaka Ueno, Katunobu Itou, Tetsushi Yada
Genome Informatics 8: 15-24 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Breakpoint Phylogenies
Mathieu Blanchette, Guillaume Bourque, David Sankoff
Genome Informatics 8: 25-34 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Sequencing by Hybridization with Positive Faults
Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Wojciech T. Markiewicz, Jan Weglarz
Genome Informatics 8: 35-42 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Greedy Algorithms for Finding a Small Set of Primers Satisfying Cover Length Resolution Conditions in PCR Experiments
Koichiro Doi, Hiroshi Imai
Genome Informatics 8: 43-52 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Prediction of Mitochondrial Targeting Signals Using Hidden Markov Model
Yukiko Fujiwara, Minoru Asogawa, Kenta Nakai
Genome Informatics 8: 53-60 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Prediction of Hydrophobic Cores of Proteins Using Wavelet Analysis
Hideki Hirakawa, Satoru Kuhara
Genome Informatics 8: 61-70 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Rhythms Emerge in a Collection of `Blind' Chemicals by the Use of `Genetic Switches'
Hiroshi Inayoshi, Hitoshi Iba
Genome Informatics 8: 71-79 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models
Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein
Genome Informatics 8: 80-89 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A New Method for Database Searching and Clustering
Antje Krause, Martin Vingron
Genome Informatics 8: 90-99 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Applying an Association Rule Discovery Algorithm to Multipoint Linkage Analysis
Nobutaka Mitsuhashi, Haretsugu Hishigaki, Toshihisa Takagi
Genome Informatics 8: 100-109 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Sequence Data Analysis for Long Disordered Regions Prediction in the Calcineurin Family
Pedro Romero, Zoran Obradovic, A. Keith Dunker
Genome Informatics 8: 110-124 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Clustering Molecular Sequences with Their Components
Sivasundaram Suharnan, Takesi Itou, Hideo Matsuda, Hirotada Mori
Genome Informatics 8: 125-134 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

DNAinsight: An Image Processing System for 2-D Gel Electrophoresis of Genomic DNA
Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe
Genome Informatics 8: 135-146 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

E-CELL: Software Environment for Whole Cell Simulation
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Tom Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison
Genome Informatics 8: 147-155 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Multi-Agent System for Exon Prediction in Human Sequences
Laurence Vignal, Frederique Lisacek
Genome Informatics 8: 156-165 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Short Talk Papers

 

Virgil: A Databank of Links between GDB and GenBank
Frederic Achard, Emmanuel Barillot
Genome Informatics 8: 166-172 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

DP Algorithms for RNA Secondary Structure Prediction with Pseudoknots
Tatsuya Akutsu
Genome Informatics 8: 173-179 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

NP-Hardness Results for Protein Side-Chain Packing
Tatsuya Akutsu
Genome Informatics 8: 180-186 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Novel Approach Towards a Comprehensive Consensus Representation of the Expressed Human Genome
Winston Hide, John Burke, Alan Christoffels, Robert Miller
Genome Informatics 8: 187-196 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

GeneMark-RC, a Recursive Procedure for Gene Identification in the Genomic Sequence Data with Self-Consistency Evaluation; Its Application to the Analysis of Several Prokaryotic Genomes
Makoto Hirosawa, Katumi Isono
Genome Informatics 8: 197-206 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

GENOME: A Networked Database Environment for Human Genome Data
Andreas M. Kogelnik, Shamkant B. Navathe, Douglas C. Wallace
Genome Informatics 8: 207-214 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Fast Discerning Repeats in DNA Sequences with a Compression Algorithm
Eric Rivals, Max Dauchet, Jean-Paul Delahaye, Olivier Delgrange
Genome Informatics 8: 215-226 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Reading Evolutionary History of Aminoacyl-tRNA Synthetases from Genome Sequences
Kiyotaka Shiba, Hiromi Motegi, Tetsuo Noda
Genome Informatics 8: 227-233 (1997)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Software Demonstration Abstracts

 

3DinSight: An Integrated Database and Search Tool for Structure, Function and Property of Biomolecules
Jianghong An, Takao Nakama, Yasushi Kubota, Akinori Sarai
Genome Informatics 8: 234-235 (1997)
[Abstract]   [Full-text PDF]

Visualization of Sequence and Biological Data in DNA Data Bank of Japan: Genome Information Broker and the Enhancement of SAKURA
Kousuke Goto, Hikaru Yamamoto, Takuro Tamura, Toshitsugu Okayama, Tomohiro Koike, Satoru Miyazaki, Hirotada Mori, Takashi Gojobori, Hideaki Sugawara
Genome Informatics 8: 236-237 (1997)
[Abstract]   [Full-text PDF]

Supporting Genome Information Processing by MetaCommander
Yasuhiko Kitamura, Tetsuya Nozaki, Shoji Tatsumi, Akira Tanigami
Genome Informatics 8: 238-239 (1997)
[Abstract]   [Full-text PDF]

A Tool on Web for Gene Regulatory Networks: Toward Software Agent for Genome Information Analysis
Hiroshi Matsuno, Manabu Hori, Nobuaki Wada, Miyako Tanaka
Genome Informatics 8: 240-241 (1997)
[Full-text PDF]

Implementing Mobile Agents in Genome Information Processing
Hiroshi Matsuno, Misako Ichimura, Tatsumi Fukuyama, Miyako Tanaka
Genome Informatics 8: 242-243 (1997)
[Full-text PDF]

Mutation View: A Distributed Database for Human Disease Gene Mutations
Shinsei Minoshima, Susumu Mitsuyama, S. Ohno, T. Kawamura, Nobuyoshi Shimizu
Genome Informatics 8: 244-245 (1997)
[Full-text PDF]

PDB Retriever: A Simple and Integrated Browser for Protein Data Bank
Tadashi Mizunuma, Sadahiko Misu, Motonori Ota, Ken Nishikawa
Genome Informatics 8: 246-247 (1997)
[Full-text PDF]

Integrated Receptor Database
Kotoko Nakata, Takako Igarashi, Tsuguchika Kaminuma
Genome Informatics 8: 248-249 (1997)
[Abstract]   [Full-text PDF]

NEXTDB: The Expression Pattern Map Database for C.elegans
Tadasu Shin-i, Yuji Kohara
Genome Informatics 8: 250-251 (1997)
[Abstract]   [Full-text PDF]

An Analysis System of 2-D Gel Electrophoresis Images for Genomic Scanning - DNAinsight -
Takayuki Toda, Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe
Genome Informatics 8: 252-253 (1997)
[Full-text PDF]

Poster Abstracts

 

Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
Genome Informatics 8: 254-255 (1997)
[Full-text PDF]

Development of a Spot Matching Module in Image Analysis System DDGEL for 2D Gel Electrophoresis
Tatsuya Akutsu, Akira Ohyama, Kyotetsu Kanaya, Asao Fujiyama
Genome Informatics 8: 256-257 (1997)
[Abstract]   [Full-text PDF]

Protein Threading Using a Score Function Derived by a Linear Programming Based Method
Tatsuya Akutsu, Hiroshi Tashimo
Genome Informatics 8: 258-259 (1997)
[Abstract]   [Full-text PDF]

Genome Scale Prediction of Two-Component Signal Transducers from the Knowledge of Regulatory Interactions
Hidemasa Bono, Susumu Goto, Hiroyuki Ogata, Minoru Kanehisa
Genome Informatics 8: 260-261 (1997)
[Abstract]   [Full-text PDF]

Detection of Intron, Exon, and Intergenic DNA in Human Genome on the Basis of Quantification Method II
Hiroki Fukasawa, Shigehiko Kanaya, Yoshihiro Kudo
Genome Informatics 8: 262-263 (1997)
[Full-text PDF]

Efficient Computation of Sequence Analysis in a Vector-Parallel Computer for the Study of Molecular Evolution
Takamasa Futatsuki, Yuichi Kawanishi, Kimitoshi Naito, Satoru Miyazaki, Hideaki Sugawara
Genome Informatics 8: 264-265 (1997)
[Abstract]   [Full-text PDF]

Translated Codons (Trons) Useful for Direct Matching of a Genomic DNA Sequence and a Protein Sequence or Profile
Osamu Gotoh
Genome Informatics 8: 266-267 (1997)
[Full-text PDF]

A Heuristic Algorithm for Genome Rearrangements
Qian-Ping Gu, Kazuyuki Iwata, Shietung Peng, Qi-Ming Chen
Genome Informatics 8: 268-269 (1997)
[Full-text PDF]

Computer Simulation of Drosophila's Early Segmentation in Virtual Drosophila ProjectShugo
Hamahashi, Hiroaki Kitano
Genome Informatics 8: 270-271 (1997)
[Abstract]   [Full-text PDF]

An Inspection of the Multiple Alignment Method with Use
Yoshitomo Harada, Masato Wayama, Toshio Shimizu
Genome Informatics 8: 272-273 (1997)
[Full-text PDF]

Automated Spot Matching in Autoradiogram Images of Two-Dimensional Electrophoresis of Genomic DNA
Junichi Isamikawa, Katsutohi Takahashi, Masayuki Nakazawa, Yasuo Watanabe
Genome Informatics 8: 274-275 (1997)
[Full-text PDF]

The Construction of the Knowledge Base on Apoptotic Molecular Interactions
Masahiro Hattori, Minoru Kanehisa
Genome Informatics 8: 276-277 (1997)
[Abstract]   [Full-text PDF]

ALIS Sequencing Database for Large Scale Human Genome Project
Mika Hirakawa, Kensaku Imai, Hiroko Yamaguchi, Junko Shimada, Kazuo Takehana, Itaru Suzuki, Masahiko Suzuki, Fumihiko Kikuchi
Genome Informatics 8: 278-279 (1997)
[Abstract]   [Full-text PDF]

Sequence Alignment with Motif Database
Susumu Hiraoka
Genome Informatics 8: 280-281 (1997)
[Full-text PDF]

Prediction Rate of Coding Regions is Enhanced upto 99.15% by Joint Use of GeneMark-RC and GeneHacker in Case of a Cyanobacterium
Makoto Hirosawa
Genome Informatics 8: 282-283 (1997)
[Full-text PDF]

Search for the Origins of Prokaryotic Cell-Division Genes
Shouken Hokari, Koji Ohnishi
Genome Informatics 8: 284-285 (1997)
[Full-text PDF]

Codon-Sensitive Comparison of DNA Sequences Containing Insertions/Deletions and Statistical Significance of the Similarity Scores
Ryotaro Irie, Naoko Kasahara, Susumu Hiraoka, Keiichi Nagai
Genome Informatics 8: 286-287 (1997)
[Abstract]   [Full-text PDF]

Function Profile: Functional Sites of Proteins Discovered by Generalization of Amino Acid Sequences
Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Yoko Kawata, Takatsugu Hirokawa
Genome Informatics 8: 288-289 (1997)
[Abstract]   [Full-text PDF]

Position Dependent Amino Acid Propensity in the Transmembrane Region for Topology Prediction of Membrane Proteins
Koji Kadota, Takatsugu Hirokawa, Shigeki Mitaku
Genome Informatics 8: 290-291 (1997)
[Abstract]   [Full-text PDF]

Establishment of Transcription Factor DataBase TFDB Maintenance System
Masako Kaizawa, Tomoko Okazaki, Hiroshi Mizushima
Genome Informatics 8: 292-293 (1997)
[Abstract]   [Full-text PDF]

Highly Sensitive Homology Search Methods on Parallel Computer
Naoko Kasahara, Susumu Hiraoka, Ryotaro Irie, Keiichi Nagai
Genome Informatics 8: 294-295 (1997)
[Abstract]   [Full-text PDF]

Automated Identification of Three-Dimensional Common Structural Features of Proteins
Hiroaki Kato, Yoshimasa Takahashi
Genome Informatics 8: 296-297 (1997)
[Abstract]   [Full-text PDF]

Construction of Molecular Interaction Database and Searching for Similar Pathways
Shuichi Kawashima, Toshiaki Katayama, Minoru Kanehisa
Genome Informatics 8: 298-299 (1997)
[Abstract]   [Full-text PDF]

Detection of Membrane Proteins in the Whole Genome Sequences
Daisuke Kihara, Minoru Kanehisa
Genome Informatics 8: 300-301 (1997)
[Abstract]   [Full-text PDF]

Biology Foundation Class Library
Koji Kyoda, Hirokaki Kitano
Genome Informatics 8: 302-303 (1997)
[Abstract]   [Full-text PDF]

Hypothesis Creator for Complete Genome
Osamu Maruyama, Hirotaka Seki, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano
Genome Informatics 8: 304-305 (1997)
[Full-text PDF]

Computer Simulation of Gene Expression by Cell-Cell Interaction Involved in Development of Drosophila's Eye
Mineo Morohashi, Hiroaki Kitano
Genome Informatics 8: 306-307 (1997)
[Abstract]   [Full-text PDF]

Gene Recognition Using Multiple Gene-Finding Programs
Katsuhiko Murakami, Toshihisa Takagi
Genome Informatics 8: 308-309 (1997)
[Abstract]   [Full-text PDF]

Some Common Statistical Features of Complete DNA Base Sequence
Nobuyuki Nakajima, Masahiro Agu, Hido Akabane
Genome Informatics 8: 310-311 (1997)
[Abstract]   [Full-text PDF]

Database and Analysis System of cDNA Sequences Obtained from Full-Length Enriched cDNA Library
Tetsuo Nishikawa, Toshio Ota, Sumio Sugano, Asaf Salamov, Yoshitaka Nakamura, Tateo Nagai, Atsushi Oogane, Yutaka Suzuki, Yuri Kawai, Shizuko Ishii, Kaoru Saito, Jun-ichi Yamamoto, Takao Isogai
Genome Informatics 8: 312-313 (1997)
[Full-text PDF]

MOLDEX: A Computer System for Drug Design 3) Constructing Hypothetical Ligand Molecules
Kouji Nishimura, Carlos Adriel Del Carpio
Genome Informatics 8: 314-315 (1997)
[Full-text PDF]

Present Status of LIGAND Chemical Database for Enzyme Reactions
Takaaki Nishioka, Susumu Goto, Minoru Kanehisa
Genome Informatics 8: 316-317 (1997)
[Full-text PDF]

Gene Finding Using HAKKE System
Kiyoshi Noda, Satoshi Matsumoto, Ayumi Shinohara, Takayoshi Shoudai, Satoru Miyano
Genome Informatics 8: 318-319 (1997)
[Full-text PDF]

Comprehensive Sequence Analysis of B.subtilis Genome Using the BSORF Database
Atsushi Ogiwara, Naotake Ogasawara, Mari Watanabe, Toshihisa Takagi
Genome Informatics 8: 320-321 (1997)
[Abstract]   [Full-text PDF]

Origins of DNA-Binding Proteins and Their Kins: A View from Poly-tRNA Theory
Koji Ohnishi, Hirokazu Tanaka, Hiroshi Yanagawa
Genome Informatics 8: 322-323 (1997)
[Full-text PDF]

p53MDB: p53 Mutation Database
Tomoko Okazaki, Kagehiko Kitano, Ikuo Uchiyama, Toshihisa Takagi
Genome Informatics 8: 324-325 (1997)
[Abstract]   [Full-text PDF]

Reconstruction of Maximum Likelihood Phylogenetic Trees in Parallel Environment Using Logic Programming
Satoshi OOta, Naruya Saitou
Genome Informatics 8: 326-327 (1997)
[Abstract]   [Full-text PDF]

Analysis of Virus Evolution Based on Inhomogeneous Markov Evolution Model
Fengrong Ren, Hiroshi Tanaka
Genome Informatics 8: 328-329 (1997)
[Abstract]   [Full-text PDF]

A Novel Method to Detect Identities in tRNA Genes Using Sequence Comparison
Jun-Ichi Sagara, Seishi Shimizu, Takeshi Kawabata, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu
Genome Informatics 8: 330-331 (1997)
[Abstract]   [Full-text PDF]

Computer Analyses of Translation Initiation Sites in Complete Genomes
Rintaro Saito, Yuko Osada, Chiyo Yasui, Masaru Tomita
Genome Informatics 8: 332-333 (1997)
[Full-text PDF]

Integrated GENES Database in KEGG
Kazushige Sato, Toyoko Katsurada, Yoshiko Kimura, Minoru Kanehisa
Genome Informatics 8: 334-335 (1997)
[Abstract]   [Full-text PDF]

A Method to Predict Transmembrane Helix Arrangements in Receptor Protein Analyzing Size-Compensated Substitution Pairs
Kiminobu Sato, Toshio Shimizu
Genome Informatics 8: 336-337 (1997)
[Abstract]   [Full-text PDF]

WebPACADE: A System for the Analysis of Structural Similarity of Protein via WWW
Kenji Satou, Toshihide Ono, Yukiko Nakanishi, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi
Genome Informatics 8: 338-339 (1997)
[Full-text PDF]

An Automatic Image Analysis System for RLGS Films
Yuichi Sugahara, Yoshihide Hayashizaki, Isao Tanihata
Genome Informatics 8: 340-341 (1997)
[Abstract]   [Full-text PDF]

GoodMotif: The System for Finding High Quality Motifs That Can Discriminate a Unique Protein Family
Makiko Suwa, Asaf Saramov, Tetsuo Nishikawa, Mark Swindells
Genome Informatics 8: 342-343 (1997)
[Abstract]   [Full-text PDF]

Database and Prediction of Sequence Motifs on Protein Molecular Interactions
Kenji Suzuki, Minoru Kanehisa
Genome Informatics 8: 344-345 (1997)
[Abstract]   [Full-text PDF]

Origin of Ribonuclease P RNA (M1 RNA)
Touru Suzuki, Ken'ichi Suwa, Hiroshi Yanagawa, Koji Ohnishi
Genome Informatics 8: 346-347 (1997)
[Full-text PDF]

Analysis of Amphiphilic Periodicity of alpha-Helices Detection of Edges of Helices and Functional Residues in Proteins
Fumi Takazawa, Minoru Kanehisa, Shigeki Mitaku
Genome Informatics 8: 348-349 (1997)
[Abstract]   [Full-text PDF]

Distribution of Significantly Repetitive Tuples Implying
Nobuyuki Uchikoga, Akira Suyama
Genome Informatics 8: 350-351 (1997)
[Abstract]   [Full-text PDF]

The Transformation Distance
Jean-Stephane Varre, Jean-Paul Delahaye, Eric Rivals
Genome Informatics 8: 352-353 (1997)
[Full-text PDF]

Assistant Software for Linkage Analysis
Yasuhiko Wada, Hiroshi Yasue
Genome Informatics 8: 354-355 (1997)
[Abstract]   [Full-text PDF]

Computer Analysis of Hairpins at Transcription Termination Sites in Procayote Genomes
Takanori Washio, Junji Sasayama, Takuya Sakaguchi, Masaru Tomita
Genome Informatics 8: 356-357 (1997)
[Full-text PDF]

Motif Analysis of Yeast Transcriptional Regulatory Regions
Tetsushi Yada, Yasushi Totoki, Kenta Nakai
Genome Informatics 8: 358-359 (1997)
[Full-text PDF]

A New Method for Analysis of DNA and Protein Sequences by 2D-Pattern Formation with Coloration
Tetushiko Yoshida, Nobuaki Obata, Kenji Oosawa
Genome Informatics 8: 360-361 (1997)
[Full-text PDF]

Integration and Analysis of Biological Data
Charlene Son
Genome Informatics 8: 362 (1997)
[Full-text PDF]

Invited Talks

 

Simple Maximum Likelihood Methods for the Optical Mapping Problem
Vlado Dancik, Michael S. Waterman
Genome Informatics 8: 1-8 (1997)
[Abstract]   [Full-text PDF]

The First Laws of Genomics
Piotr P. Slonimski
Genome Informatics 8: 9-10 (1997)

Invited Talk
Jerome Chailloux
Genome Informatics 8: 11 (1997)
[Full-text PDF]

The Map of the Cell is in the Chromosome
Antoine Danchin, Alain Henaut
Genome Informatics 8: 13-14 (1997)
[Full-text PDF]