Genome Informatics Vol. 7 (1996)

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Genome Informatics Vol. 7 (1996)

Presented at the Genome Informatics Workshop 1996
December 2-3, 1996, Yebisu Garden Place, Tokyo, Japan

Published as: Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S. and Nakai, K. (eds.) "Genome Informatics 1996"
Universal Academy Press, Tokyo, 1996

Preface by Tatsuya Akutsu

 

 


 

Oral Session

 

On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies
Louxin Zhang
Genome Informatics 7: 1-12 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Approximation algorithms for genome rearrangements
Qian-Ping Gu, Shietung Peng, Hal Sudborough
Genome Informatics 7: 13-22 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A clustering method for molecular sequences based on pairwise similarity
H. Matsuda, T. Ishihara, A. Hashimoto
Genome Informatics 7: 23-32 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Approximate multiple strings searching by clustering
Fei Shi, Peter Widmayer
Genome Informatics 7: 33-40 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Parametric alignment of multiple biological sequences
Tetsuo Shibuya, Hiroshi Imai
Genome Informatics 7: 41-50 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Finding minimal multiple generalization over regular patterns with alphabet indexing
Michiyo Yamaguchi, Shinichi Shimozono, Takeshi Shinohara
Genome Informatics 7: 51-60 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Systematization of species-specific diversity of genes in codon usage: Comparison of the diversity among bacteria and prediction of the protein production levels in cells
Shigehiko Kanaya, Yoshihiro Kudo, Shinya Suzuki, Toshimichi Ikemura
Genome Informatics 7: 61-71 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis
Kenta Nakai
Genome Informatics 7: 72-81 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

An algorithm for highly specific recognition of protein-coding regions
M. S. Gelfand, T. V. Astakhova, M. A. Roytberg
Genome Informatics 7: 82-87 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Finding genes by hidden Markov models with a protein motif dictionary
Kiyoshi Asai, Tetsushi Yada, Katunobu Itou
Genome Informatics 7: 88-97 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

HAKKE: a multi-strategy prediction system for sequences
Naohiro Furukawa, Satoshi Matsumoto, Ayumi Shinohara, Takayoshi Shoudai, Satoru Miyano
Genome Informatics 7: 98-107 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Modeling proteins conformation in solution. Part I: a parallel GA engine for protein conformational space mapping
Carlos A. Del Carpio, Valentin Gogonea
Genome Informatics 7: 108-118 (1996)
[Abstract]   [Full-text HTML]  

Effect of secondary structure prediction on protein fold recognition and database search
Nickolai N. Alexandrov, Victor V. Solovyev
Genome Informatics 7: 119-127 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Analysis of binary relations and hierarchies of enzymes in the metabolic pathways
Hiroyuki Ogata, Hidemasa Bono, Wataru Fujibuchi, Susumu Goto, Minoru Kanehisa
Genome Informatics 7: 128-136 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

MetaViewer and MetaCommander: WWW tools for genome informatics
Yasuhiko Kitamura, Hideyuki Nakanishi, Tetsuya Nozaki, Teruhisa Miura, Toru Ishida
Genome Informatics 7: 137-146 (1996)
[Abstract]   [Full-text HTML]  

FOREST, a browser for huge DNA sequences
R. Gras, J. Nicolas
Genome Informatics 7: 147-156 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Development of new DDBJ DNA sequence database with data annotation
Tomohiro Koike, et al.
Genome Informatics 7: 157-165 (1996)
[Abstract]   [Full-text HTML]   [Full-text PDF]

 

Poster Session

 

A taxonomy database system for managing multimedia contents
Hajime Kitakami, Yasuma Mori, Masatoshi Arikawa
Genome Informatics 7: 166-167 (1996)
[Abstract]   [Full-text PDF]

Automated identification of three-dimensional motif in proteins
Hiroaki Kato, Yoshimasa Takahashi
Genome Informatics 7: 168-169 (1996)
[Abstract]   [Full-text PDF]

Characterization of enzyme structure by informational complexity
Takayuki Kamei, Yasuo Yonezawa
Genome Informatics 7: 170-171 (1996)
[Abstract]   [Full-text PDF]

Java version of animal genome database
Y. Wada, H. Yasue
Genome Informatics 7: 172-173 (1996)
[Abstract]   [Full-text PDF]

A symbolic representation for RNA secondary structures; towards the construction of RNA secondary structures data base
A. Nakaya, A. Yonezawa, K. Yamamoto
Genome Informatics 7: 174-175 (1996)
[Full-text PDF]

Multiple sequence alignment using a genetic algorithm
Masamichi Isokawa, Masato Wayama, Toshio Shimizu
Genome Informatics 7: 176-177 (1996)
[Full-text PDF]

Discovering functional sites of amino acid sequences using sorted variable generalization
Takashi Ishikawa, Shigeki Mitaku, Takao Terano
Genome Informatics 7: 178-179 (1996)
[Abstract]   [Full-text PDF]

Improvement of the transmembrane helix prediction system by three-stage model
Takatsugu Hirokawa, Seah Boon-Chieng, Shigeki Mitaku
Genome Informatics 7: 180-181 (1996)
[Abstract]   [Full-text PDF]

Sequence analysis of short tandem repeats in the genomes of H.influenzae and M.genitalium
Takanori Washio, Masahiko Wada, Masaru Tomita
Genome Informatics 7: 182-183 (1996)
[Full-text PDF]

On correlation between G+C contents and introns lengths: Longer introns tend to be more A+T rich
Yasuhiro Asakawa, Masaru Tomita
Genome Informatics 7: 184-185 (1996)
[Abstract]   [Full-text PDF]

CpG dinucleotide distribution and DNA methylation
Tom Shimizu, Kouichi Takahashi, Masaru Tomita
Genome Informatics 7: 186-187 (1996)
[Full-text PDF]

Computer analyses of nucleotide patterns around start codons
Rintaro Saito, Hidekazu Sasaki, Yuko Osada, Masaru Tomita
Genome Informatics 7: 188-189 (1996)
[Full-text PDF]

Computer analyses of overlapping genes in Mycoplasma genitalium
Yuko Osada, Ryo Matsushima, Masaru Tomita
Genome Informatics 7: 190-191 (1996)
[Full-text PDF]

Computer analyses of site-specific variabilities in human Alu sequences
Michiko Muraki, Masaru Tomita
Genome Informatics 7: 192-193 (1996)
[Full-text PDF]

Inferring history of genomic duplication using subclassified Alu elements
Yoshimi Toda, Masaru Tomita
Genome Informatics 7: 194-195 (1996)
[Full-text PDF]

Motif extraction: Normalization of scores
Y. Fujiwara, M. Asogawa
Genome Informatics 7: 196-197 (1996)
[Abstract]   [Full-text PDF]

Beta-sheet prediction using inter-strand residue pairs and refinement with Hopfield neural network
Minoru Asogawa
Genome Informatics 7: 198-199 (1996)
[Full-text PDF]

Building a receptor database
K. Nakata, M. Hayakawa, T. Igarashi, T. Kaminuma
Genome Informatics 7: 200-201 (1996)
[Abstract]   [Full-text PDF]

Direct comparison DNA and amino acid sequences based on a dynamic programming method
Naoko Kasahara, Susumu Hiraoka, Keiichi Nagai
Genome Informatics 7: 202-203 (1996)
[Abstract]   [Full-text PDF]

SAKURA: A new data submission system of DDBJ to meet users' needs in the age of mass production of DNA sequences
Hikaru Yamamoto, Takuro Tamura, Katsumi Isono, Takashi Gojobori, Hideaki Sugawara, Ken Nishikawa, Naruya Saitou, Tadashi Imanishi, Kaoru Fukami-Kobayashi, Kazuho Ikeo, Yoshio Tateno
Genome Informatics 7: 204-205 (1996)
[Full-text PDF]

Emergent rhythms in an artificial chemical world using 'genetic switches'
Hiroaki Inayoshi, Hitoshi Iba
Genome Informatics 7: 206-207 (1996)
[Abstract]   [Full-text PDF]

A new software for visualization of large proteins
Yutaka Ueno, Kiyoshi Asai
Genome Informatics 7: 208-209 (1996)
[Abstract]   [Full-text PDF]

Automatic discovery of hidden Markov representations for functional sites within DNA sequences
Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai
Genome Informatics 7: 210-211 (1996)
[Full-text PDF]

GeneHacker: "Gene-finding program for the prediction of precise protein coding regions
Makoto Hirosawa, Tetsushi Yada
Genome Informatics 7: 212-213 (1996)
[Full-text PDF]

CyanoBase: The genome database for Synechocystis sp. strain PCC6803
Yasukazu Nakamura, Nobuyuki Miyajima, Makoto Hirosawa, Takakazu Kaneko, Satoshi Tabata
Genome Informatics 7: 214-215 (1996)
[Full-text PDF]

Management system for sequencing data of human genome - as a part of ALIS -
Mika Hirakawa, Kensaku Imai, Akira Ohyama, Fumihiko Kikuchi
Genome Informatics 7: 216-217 (1996)
[Abstract]   [Full-text PDF]

Establishment and management of transcription factor database TFDB
T. Okazaki, M. Kaizawa, H. Mizushima
Genome Informatics 7: 218-219 (1996)
[Abstract]   [Full-text PDF]

Very fast identification of tRNA in genomic DNA
F. Lisacek, N. El Mabrouk
Genome Informatics 7: 220-221 (1996)
[Full-text PDF]

Predicting and learning RNA secondary structures
Aki Hasegawa, Yasuo Uemura, Satoshi Kobayashi, Takashi Yokomori
Genome Informatics 7: 222-223 (1996)
[Abstract]   [Full-text PDF]

Modeling proteins conformation in solution. Part II: a solvent effect model based on the evaluation of solvent-accessible surface area and generalized Born equation
Valentin Gogonea, Camelia Baleanu-Gogonea, Carlos A. Del Carpio
Genome Informatics 7: 224-225 (1996)
[Abstract]   [Full-text PDF]

Sense-antisense homology boxes in proteins: Structural motifs enconded in the DNA?
Carlos A. Del Carpio, Valentin Gogonea, Katsuhisa Yamaguchi, Makoto Takei, Kouji Nishimura
Genome Informatics 7: 226-227 (1996)
[Abstract]   [Full-text PDF]

Construction of the Bacillus subtilis ORF database BSORF DB
A. Ogiwara, N. Ogasawara, M. Watanabe, T. Takagi
Genome Informatics 7: 228-229 (1996)
[Full-text PDF]

Clustering and evolutional analysis of E. coli proteins
Suharnan Sivasundaram, Jun-ichi Takeda, Takeshi Itoh, Keiko Takemoto, Hidemi Watanabe, Hideo Matsuda, Hirotada Mori
Genome Informatics 7: 230-231 (1996)
[Full-text PDF]

High-speed genome scanning analysis based on automated detection and matching spots in autoradiogram images of 2-D gel electrophoresis
Tomoyasu Takahashi, Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe
Genome Informatics 7: 232-233 (1996)
[Abstract]   [Full-text PDF]

The inference of model-based minimum complexity in reconstructing molecular phylogenetic tree
F. Ren, H. Tanaka, T. Okayama
Genome Informatics 7: 234-235 (1996)
[Abstract]   [Full-text PDF]

3DInSight: An integrated relational database and search tool for molecular structures and functional sites
J. An, T. Nakama, Y. Kubota, A. Sarai
Genome Informatics 7: 236-237 (1996)
[Full-text PDF]

Poly-tRNA structure in the Bacilluis subtilis rrnB operon is a relic of an early peptide-synthesizing ribozyme co-ancestral to the E. coli trpE gene and the exon 2 of the chicken triose-phosphate isomerase gene
Koji Ohnishi, Hiroshi Yanagawa
Genome Informatics 7: 238-239 (1996)
[Full-text PDF]

Mutation View: A network-transparent database system for mutations in the human disease genes
S. Minoshima, S. Mitsuyama, N. Shimizu
Genome Informatics 7: 240-241 (1996)
[Full-text PDF]

Vestiges of primordial words in base sequences of modern genomes
Nobuyuki Uchikoga, Akira Suyama
Genome Informatics 7: 242-243 (1996)
[Abstract]   [Full-text PDF]

A prediction method for transmembrane segments in proteins utilizing multiple discrimination functions
Daisuke Kihara, Toshio Shimizu, Minoru Kanehisa
Genome Informatics 7: 244-245 (1996)
[Abstract]   [Full-text PDF]

A statistical analysis of gene arrangement patterns in bacterial and yeast genomes
Kentaro Tomii, Minoru Kanehisa
Genome Informatics 7: 246-247 (1996)
[Abstract]   [Full-text PDF]

Standard Gibbs free energy changes of enzyme reactions in metabolic pathway computation
Susumu Goto, Nobuhiro Fukushima, Minoru Kanehisa
Genome Informatics 7: 248-249 (1996)
[Abstract]   [Full-text PDF]

Deductive calculation library for KEGG pathway simulation
Wataru Fujibuchi, Susumu Goto, Minoru Kanehisa
Genome Informatics 7: 250-251 (1996)
[Abstract]   [Full-text PDF]

Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions
Hidemasa Bono, Hihoyuki Ogata, Susumu Goto, Minoru Kanehisa
Genome Informatics 7: 252-253 (1996)
[Abstract]   [Full-text PDF]

Java applets for handling genome maps in KEGG
Kazushige Sato, Toyoko Katsurada, Tomomi Kamiya, Mayuko Egoshi, Minoru Kanehisa
Genome Informatics 7: 254-255 (1996)
[Abstract]   [Full-text PDF]

Finding coding region using secondary hexamer measure and two-dimensional linear discriminant analysis
Katsuhiko Murakami, Toshihisa Takagi
Genome Informatics 7: 256-257 (1996)
[Abstract]   [Full-text PDF]

Information finding from biological papers
Yoshihiro Ohta, Yasunori Yamamoto, Ikuo Uchiyama, Toshihisa Takagi
Genome Informatics 7: 258-259 (1996)
[Abstract]   [Full-text PDF]

Constructing a dictionary of biological terms for information extraction
Yasunori Yamamoto, Yoshihiro Ohta, Ikuo Uchiyama, Toshihisa Takagi
Genome Informatics 7: 260-261 (1996)
[Abstract]   [Full-text PDF]

A refinement system for large amount of cDNA data
Haretsugu Hishigaki, Kagehiko Kitano, Yusuke Nakamura, Hiroumi Maekawa, Toshihisa Takagi
Genome Informatics 7: 262-263 (1996)
[Abstract]   [Full-text PDF]

Automatic classification of protein structures with deductive database system
Yoshihisa Yamamura, Yukiko Tsukamoto, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara
Genome Informatics 7: 264-265 (1996)
[Full-text PDF]

Application of data mining to genetic linkage analysis
Nobutaka Mitsuhashi, Haretsugu Hishigaki, Toshihisa Takagi
Genome Informatics 7: 266-267 (1996)
[Abstract]   [Full-text PDF]

Mining binary diagram rules
Kazuya Inoue, Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano
Genome Informatics 7: 268-269 (1996)
[Full-text PDF]

A PAC-learning algorithm for conformation rules and its experiments
Osamu Maruyama, Erika Tateishi, Emiko Furuichi, Satoru Kuhara, Satoru Miyano
Genome Informatics 7: 270-271 (1996)
[Full-text PDF]

An image analysis system for two-dimensional gel electrophoresis
Akira Ohyama, Kyotetsu Kanaya, Tatsuya Akutsu, Asao Fujiyama
Genome Informatics 7: 272-273 (1996)
[Full-text PDF]

Multiple alignment of biological sequences containing tandem repeat
Hidetoshi Kitada, Kazuhiro Tono, Masahito Yamamoto, Tamotsu Mitamura, Azuma Ohuchi, Toshio Ohyanagi, Norio Matsushima
Genome Informatics 7: 274-275 (1996)
[Abstract]   [Full-text PDF]

Harmonic analysis of protein sequences
Meeta Rani, Chanchal K. Mitra
Genome Informatics 7: 276-277 (1996)
[Full-text PDF]

 

Invited Lectures

 

Failures of inverse folding and threading with gapped alignment
Gordon M. Crippen
Genome Informatics 7: 278 (1996)
[Full-text PDF]

Transforming men into mice
Pavel A. Pevzner
Genome Informatics 7: 279 (1996)
[Full-text PDF]

Toward computer-aided biology: A synthetic approach for understanding life
Hiroaki Kitano
Genome Informatics 7: 280 (1996)
[Full-text PDF]

Virtual reality and tele-existence
Susumu Tachi
Genome Informatics 7: 281 (1996)
[Full-text PDF]