Introduction We developed an algorithm that classifies all observed units of alternative splicing and transcriptional initiation and termination (UASTs) into an extendable set of distinct elementary...
Genome Informatics 14: 555--556 (2003) 555 Bioinformatics Studies on Transmembrane Strand (2004)
M. Michael Gromiha, Shandar Ahmad, Makiko Suwa
Introduction Outer membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing the molecules like maltose and...
Genome Informatics 14: 565--566 (2003) 565 Correlated Mutation Analysis of C2H2 Zinc Finger (2004)
Takafumi Nagano, Makiko Suwa, Kiyoshi Asai
Introduction Zinc finger proteins perform various functions in cellular processes, such as transcription, translation, metabolism and signaling, by binding to nucleic acids or proteins. In a zinc...
Genome Informatics 14: 412--413 (2003) Human Full-Length Pre-mRNA Sequence Dataset for (2004)
Masahiko Mizuno, Osamu Gotoh, Makiko Suwa
Introduction Computational gene prediction has recently become essential to identify all the genes from enormous genome sequences and to define their functions. However, gene prediction methods still...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Gene Discovery of G-Protein Coupled Receptors from Human Genome (2001)
Human Genome, Makiko Suwa, Toshiyuki Sato, Ikuo Okouchi, Masamitsu Mikoshiba, Yutaka Akiyama, ...
Introduction In this summer/2000,mom than 90%o humangenoG sequences had becoD availableto use, and this enco9DH/H researchersto challenge thedisco veryo no vel genesfro humangenovG Here, the moU...
An Integrated Analysis and Database System for Full-Length cDNA (2001)
Tetsuo Nishikawa, Katsuhiko Murakami, Naoyuki Harada, Toshio Ota, Tomoyasu Sugiyama, Keiichi Nagai, ...
Annotation and databasesystem of full-length cDNA sequences was developed. As the com ponents of thesystem ORF annotationsystem functional annotationsystem based on database search results,msults...
Genome Analysis: Assigning Protein Coding Regions to 3D Structures (1998)
Asaf A. Salamov, Makiko Suwa, Christine A. Orengo, Mark B. Swindells
Introduction The advent of complete genome sequencing has emphasised the need for comparable developments in automated analysis, for finding approximate 3D structure of a protein combined with the...
Genome Analysis: Assigning Protein Coding Regions to 3D Structures (1998)
Asaf A. Salamov, Makiko Suwa, Christine A. Orengo, Mark B. Swindells
Introduction The advent of complete genome sequencing has emphasised the need for comparable developments in automated analysis, for finding approximate 3D structure of a protein combined with the...
Building a Knowledge-Base for Protein Function Prediction using Multistrategy Learning (1995)
Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Takatsugu Hirokawa, Makiko Suwa, Seah Boon Ching
Conventional techniques for protein function prediction using similarities of amino acid sequences enable us to only classify the protein functions into function groups. They usually fail to predict...
Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku
orkstation, IRIS 4D/35. Conformational search of lateral positioning on some lattice fields: The first step for modelling is the search of preferable positioning in triangular unit. Because it is...
The Prediction of Lateral and Rotational Positioning of (1995)
Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku
Introduction A new method for the prediction of the lateral and the rotational positioning of transmembrane helices was developed[1] and applied to the amino acid sequence of bacteriorhodopsin. The...
Finding Functional Features of Proteins (1995)
Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Takatsugu Hirokawa, Makiko Suwa, Seah Boon Chieng
Protein function prediction from amino-acid sequences is one of the major tasks in genome informatics. To predict protein functions of a given amino-acid sequence, we can use similarities among...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Nakao, Mitsuteru, Barrero, Roberto A., Mukai, Yuri, Motono, Chie, Suwa, Makiko, Nakai, Kenta
We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further,...
TMBETA-NET: discrimination and prediction of membrane spanning β-strands in outer membrane proteins
Gromiha, M. Michael, Ahmad, Shandar, Suwa, Makiko
We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning β-strand segments. The amino acid compositions of globular and outer...
Yabuki, Yukimitsu, Muramatsu, Takahiko, Hirokawa, Takatsugu, Mukai, Hidehito, Suwa, Makiko
We describe a novel system, GRIFFIN (G-protein and Receptor Interaction Feature Finding INstrument), that predicts G-protein coupled receptor (GPCR) and G-protein coupling selectivity based on a...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Nakao, Mitsuteru, Barrero, Roberto A., Mukai, Yuri, Motono, Chie, Suwa, Makiko, Nakai, Kenta
We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further,...
TMBETA-NET: discrimination and prediction of membrane spanning β-strands in outer membrane proteins
Gromiha, M. Michael, Ahmad, Shandar, Suwa, Makiko
We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning β-strand segments. The amino acid compositions of globular and outer...
Yabuki, Yukimitsu, Muramatsu, Takahiko, Hirokawa, Takatsugu, Mukai, Hidehito, Suwa, Makiko
We describe a novel system, GRIFFIN (G-protein and Receptor Interaction Feature Finding INstrument), that predicts G-protein coupled receptor (GPCR) and G-protein coupling selectivity based on a...
TMBETA-GENOME: database for annotated β-barrel membrane proteins in genomic sequences
Gromiha, M. Michael, Yabuki, Yukimitsu, Kundu, Srinesh, Suharnan, Sivasundaram, Suwa, Makiko
We have developed the database, TMBETA-GENOME, for annotated β-barrel membrane proteins in genomic sequences using statistical methods and machine learning algorithms. The statistical methods are...