Genome Informatics Vol. 6 (1995)

Presented at the Genome Informatics Workshop 1995
December 11-12, 1995, Yokohama, Japan

Published as: M. Hagiya, S. Miyano, K. Nakai, A. Suyama, T. Yokomori and T. Takagi (eds.) "Genome Informatics 1995"
Universal Academy Press, Tokyo, 1995

Preface by Masami Hagiya


Oral Session

Protein Structure Alignment Using a Graph Matching Technique
Tatsuya Akutsu
Genome Informatics 6: 1-8 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

k-Group Multiple Alignment Based on A* Search
Hiroshi Imai, Takahiro Ikeda
Genome Informatics 6: 9-18 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Construction of Phylogenetic Trees from Amino Acid Sequences using Genetic Algorithm
Hideo Matsuda
Genome Informatics 6: 19-28 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

SIMFLY2: Simulation of a Fly Embryo
Masanori Arita
Genome Informatics 6: 29-38 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Building a Knowledge-Base for Protein Function Prediction using Multistrategy Learning
Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Takatsugu Hirokawa, Makiko Suwa, Seah Boon-Chien
Genome Informatics 6: 39-48 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

A Data and Knowledge Base for Cell Signaling Networks
Takako Igarashi, Yoko Nadaoka, Tsuguchika Kaminuma
Genome Informatics 6: 49-56 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Automated Discovery of Protein Functional Units from Amino-acid sequences using Rough-Sets-based Comparative Analysis
Shusaku Tsumoto, Hiroshi Tanaka, Kohei Tsumoto, Izumi Kumagai
Genome Informatics 6: 57-66 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Grammatically Modeling and Predicting RNA Secondary Structures
Yasuo Uemura, Aki Hasegawa, Satoshi Kobayashi, Takashi Yokomori
Genome Informatics 6: 67-76 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Hidden Markov Model to Extract Leucine Zipper Motif
Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya
Genome Informatics 6: 77-85 (1995)
[Abstract]  [Full-text HTML]   [Full-text PDF]

Poster Session

Assessment of Species-specific Diversity of Genes in Codon Usage
Shigehiko Kanaya, Yoshihiro Kudo, Yasukazu Nakamura, Toshimichi Ikemura
Genome Informatics 6: 86-87 (1995)
[Abstract]   [Full-text PDF]

Estimation of Protein-production levels in Escherichia coli Genes on the basis of Multivariate Diversity in Codon Usage
Shigehiko Kanaya, Yoshihiro Kudo, Yasukazu Nakamura, Toshimichi Ikemura
Genome Informatics 6: 88-89 (1995)
[Abstract]   [Full-text PDF]

Consensus Genic Sequences in Bacterial rRNA-tRNA gene clusters
Yoshihiro Kudo, Shigehiko Kanaya
Genome Informatics 6: 89-90 (1995)
[Abstract]   [Full-text PDF]

MDL Method: an Inductive Inference Method for Reconstructing Phylogenetic Trees
Fengrong Ren, Hiroshi Tanaka, Norio Fukuda
Genome Informatics 6: 92-93 (1995)
[Abstract]   [Full-text PDF]

Clustering of all known and predicted open reading frames of Escherichia coli K12
Takeshi Itoh, Minoru Yano, Keiko Takemoto, Miwako Kajihara, Hirotada Mori
Genome Informatics 6: 94-95 (1995)
[Abstract]   [Full-text PDF]

Statistical features identified from comparison of homologous introns
Hiroyuki Ogata, Wataru Fujibuchi, Minoru Kanehisa
Genome Informatics 6: 96-97 (1995)
[Abstract]   [Full-text PDF]

Evalutation of exon prediction tools using a long DNA sequence data
Katsuhiko Murakami, Shiho Tsukumi, Toshihisa Takagi, Masahira Hattori
Genome Informatics 6: 98-99 (1995)
[Abstract]   [Full-text PDF]

Comparison of Statistical Algorithms for Predicting Splice Junctions in mRNA Precursors of Mammalian Genes
Yukiyasu Ogawa, Tomomasa Nagashima, Sirajuddin Khawaja
Genome Informatics 6: 100-101 (1995)
[Abstract]   [Full-text PDF]

CyanoBase: Visual Presentation of information on the genome of Cynabacterium Synechocysis sp. train PCC9803 through WWW
Makoto Hirosawa, Takakazu Kaneko, Satoshi Tabata
Genome Informatics 6: 102-103 (1995)
[Abstract]   [Full-text PDF]

A large-scale GenBank search of Expressed Sequence Tags using rapid identity searching program for DNA sequences
Tetsuo Nishikawa, Keiichi Ngai
Genome Informatics 6: 104-105 (1995)
[Abstract]   [Full-text PDF]

Prediction of Promoter Expression Specificity by Conserved Sequence Patterns
Wataru Fujibuchi, Minoru Kanehisa
Genome Informatics 6: 106-107 (1995)
[Abstract]   [Full-text PDF]

Mining Association Rules from Signals found in Mammalian Promoter Sequences
Gen Shibayama, Kenji Sato, Toshihisa Takagi
Genome Informatics 6: 108-109 (1995)
[Abstract]   [Full-text PDF]

HAKKE: Automatic Predictor Generator for Sequences
Naohiro Furukawa, Takayoshi Shoudai, Ayumi Shinohara, Satoru Miyano
Genome Informatics 6: 110-111 (1995)
[Abstract]   [Full-text PDF]

Learning Hidden Markov Models Using Back-Propagation through Time
Hiroshi Mamitsuka
Genome Informatics 6: 112-113 (1995)
[Abstract]   [Full-text PDF]

A Probabilistic Inference System for The Prediction of Subcellular Localization Sites of Proteins: Application to E. coli Data
Paul Horton, Kenta Nakai
Genome Informatics 6: 114-115 (1995)
[Abstract]   [Full-text PDF]

Protein Sequence Grouping by Peptide Word Motifs
Ikuo Ichiyama, Atsushi Ogiwara, Toshihisa Takagi, Minoru Kanehisa
Genome Informatics 6: 116-117 (1995)
[Abstract]   [Full-text PDF]

Antisense Homology Boxes in Proteins
Lajos Baranyi, William Campbell, Hidechika Okada
Genome Informatics 6: 118-119 (1995)
[Abstract]   [Full-text PDF]

Multiple sequence alignment by combining incomplete blocks of similar segments
Kenji Suzuki, Yutaka Akiyama, Minoru Kanehisa
Genome Informatics 6: 120-121 (1995)
[Abstract]   [Full-text PDF]

An Approach to Amino Acid Sequence Alignment Using a Genetic Algorithm
Masato Wayama, Katsutoshi Takahashi, Toshio Shimizu
Genome Informatics 6: 122-123 (1995)
[Abstract]   [Full-text PDF]

Accuracy of multiple sequence alignment as assessed by reference to structural alignments
Osamu Gotoh
Genome Informatics 6: 124-125 (1995)
[Abstract]   [Full-text PDF]

Design of a Hardware Board for Sequence Alignment
Tsuyoshi Kato, Makoto Taiji, Toshikazu Ebisuzaki, Akira Suyama
Genome Informatics 6: 126-127 (1995)
[Abstract]   [Full-text PDF]

Theoretical Prediction of Positioning, Orientation and Tilt Angles of Helices of a Small Membrane Protein Without Structural Template
Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku
Genome Informatics 6: 128-129 (1995)
[Abstract]   [Full-text PDF]

A Parallel Hybrid GA for Peptide 3-D Structure Prediction
Carlos A. Del Carpio, Shin-ichi Sasaki, Lajos Baranyi, Hidechika Okada
Genome Informatics 6: 130-131 (1995)
[Abstract]   [Full-text PDF]

Three-Dimensional Motif Search of Proteins Using Abstract Representation of Secondary Structure Segment
Hiroaki Kato, Yoshimasa Takahashi
Genome Informatics 6: 132-133 (1995)
[Abstract]   [Full-text PDF]

β-sheet Prediction using Inter-strand Residue Pair Propensities
Minoru Asogawa
Genome Informatics 6: 134-135 (1995)
[Abstract]   [Full-text PDF]

A Study of Molecular Recognition between DNA and Metal Ions
Nobuhiro Fukushima, Minoru Kanehisa
Genome Informatics 6: 136-137 (1995)
[Abstract]   [Full-text PDF]

LIGAND Chemical Database for Enzymatic Reactions: A Link between enzyme structures and chemical reactions
Takaaki Nishioka, Mikita Suyama, Susumu Goto, Yutaka Akiyama
Genome Informatics 6: 138-139 (1995)
[Abstract]   [Full-text PDF]

Receptor Database Representation
Kotoko Nakata, Masataka Hayakawa, Tatsuya Nakano, Tsuguchika Kaminuma
Genome Informatics 6: 140-141 (1995)
[Abstract]   [Full-text PDF]

AAindex : A Database of Amino Acid Indices and Mutation Matrices
Kentaro Tomii, Minoru Kanehisa
Genome Informatics 6: 142-143 (1995)
[Abstract]   [Full-text PDF]

Workstation Session

A Software Tool for Mapping Human Genome by Chromosome-Specific Two-Dimensional Electrophoresis Method
Akira Ohyama, Tatsuya Akutsu, Asao Fujiyama
Genome Informatics 6: 144-145 (1995)
[Abstract]   [Full-text PDF]

GeneViewPLUS, Locus-in and Physical Mapper: The GUI-softwares for genome mapping data management
Shinsei Minoshima, Susumu Mitsuyama, Kazuhiko Kawasaki, Nobuyoshi Shimizu
Genome Informatics 6: 146-147 (1995)
[Abstract]   [Full-text PDF]

gRanch: Gene Mapping Workbench
Yasuhiko Wada, Kengo Inoue, Hiroshi Ohga, Hiroshi Yasue
Genome Informatics 6: 148-149 (1995)
[Abstract]   [Full-text PDF]

An Integrated System for Large-Scale Sequencing: Dr.AGCT
Zhongqing Wang, Akira Ohyama, Nobuyuki Miyajima
Genome Informatics 6: 150-151 (1995)
[Abstract]   [Full-text PDF]

DNA sequence comparison based on amino acid similarity
Susumu Hiraoka, Keiichi Nagai
Genome Informatics 6: 152-153 (1995)
[Abstract]   [Full-text PDF]

Prediction of Transmembrane Helical Regions by Three-stage Model
Seah Boon-Chien, Shigeki Mitaku
Genome Informatics 6: 154-155 (1995)
[Abstract]   [Full-text PDF]

Experiments by BONSAI Garden
Naohiro Furukawa, Erika Tateishi, Takayoshi Shodai, Satoru Miyano
Genome Informatics 6: 156-157 (1995)
[Abstract]   [Full-text PDF]

A WWW Tool for Organizing Knowledge of Biomolecular Reaction Pathways
Nobuo Tsukamoto, Minoru Kanehisa
Genome Informatics 6: 158-159 (1995)
[Abstract]   [Full-text PDF]

An integrated database SPAD(Signaling PAthway Database) for signal transduction and genetic information
Naoko Tateishi, Haruki Shiotari, Satoru Kuhara, Toshihisa Takagi, Minoru Kanehisa
Genome Informatics 6: 160-161 (1995)
[Abstract]   [Full-text PDF]

A WWW Database of Bacillus Subtilis ORFs determined by the International Project of Sequencing B. Subtilis Genome
Atsushi Ogiwara, Toshihisa Takagi, Naotake Ogasawara
Genome Informatics 6: 162-163 (1995)
[Abstract]   [Full-text PDF]

Developing Sequence Analysis Tools on Web Server
Teruo Yasunaga, Tatsuya Takagi, Atsushi Takeuchi, Toshiyuki Niiyama
Genome Informatics 6: 164-165 (1995)
[Abstract]   [Full-text PDF]

Fop (frequency of optimal codon usage): WWW service with its distribution analysis
Yasukazu Nakamura, Toshimichi Ikemura
Genome Informatics 6: 166-167 (1995)
[Abstract]   [Full-text PDF]

Invited Lectures

Combinatorial Problems in Physical Mapping
Richard M. Karp
Genome Informatics 6: 168-169 (1995)
[Full-text PDF]

From Genotype to Phenotype: Navigating Nature's Information Landscape at NCBI
David Lipman
Genome Informatics 6: 170 (1995)
[Full-text PDF]

The computer and the fly - FlyBase
Michael Ashburner
Genome Informatics 6: 171-172 (1995)
[Full-text PDF]

Synaptic Specificity Between Embryonic Motoneurons and Muscles Are Mediated by "Boolean" Combinatorial Mechanisms Among Recognition Molecules
Yoshiki Hotta
Genome Informatics 6: 173-174 (1995)
[Full-text PDF]

From Augmentation Media to Meme Media: Towards a New Knowledge Media Architecture
Yuzuru Tanaka
Genome Informatics 6: 175-177 (1995)
[Full-text PDF]