H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts (2009)
Chisato Yamasaki, Katsuhiko Murakami, Jun-ichi Takeda, Yoshiharu Sato, Akiko Noda, Ryuichi Sakate, ...
H-Invitational Database (H-InvDB; "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human...
DDBJ Activities: Contribution to the Research in Information Biology (2009)
Jun Mashima, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho Ikeo, Hideaki Sugawara, ...
DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International...
Fukuchi, Satoshi, Homma, Keiichi, Minezaki, Yoshiaki, Gojobori, Takashi, Nishikawa, Ken
Abstract Background In addition to structural domains, most eukaryotic proteins possess intrinsically disordered (ID) regions. Although ID regions often play important functional roles, their...
Genome Network Project: An Integrated Genomic Platform (2009)
Jose C. Clemente, So Nakagawa, Kazuho Ikeo, Takashi Gojobori
With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on...
Optimized ancestral state reconstruction using Sankoff parsimony (2009)
Clemente, José C, Ikeo, Kazuho, Valiente, Gabriel, Gojobori, Takashi
Abstract Background Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of...
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts (2009)
Shimada, Makoto K., Matsumoto, Ryuzou, Hayakawa, Yosuke, Sanbonmatsu, Ryoko, Gough, Craig, Yamaguchi-Kabata, Yumi, ...
Creation of a vast variety of proteins is accomplished by genetic variation and a variety of alternative splicing transcripts. Currently, however, the abundant available data on genetic variation and...
DDBJ dealing with mass data produced by the second generation sequencer (2009)
Sugawara, Hideaki, Ikeo, Kazuho, Fukuchi, Satoshi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period...
Fukuchi, Satoshi, Homma, Keiichi, Sakamoto, Shigetaka, Sugawara, Hideaki, Tateno, Yoshio, Gojobori, Takashi, ...
The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and...
Midline governs axon pathfinding by coordinating expression of two major guidance systems (2009)
Liu, Qing-Xin, Hiramoto, Masaki, Ueda, Hitoshi, Gojobori, Takashi, Hiromi, Yasushi, Hirose, Susumu
Formation of the neural network requires concerted action of multiple axon guidance systems. How neurons orchestrate expression of multiple guidance genes is poorly understood. Here, we show that...
Agrobiological Resources (2008)
Ha. Jime Kitakami, Tadasu Shin-i, Kazuho Ikeo, Yoshihiro Ugawa, Naruya Saitou, Takashi Gojobori, ...
305, Japan Recently, we newly developed a relrrtionrrl schema for eflectively building, integruting. and searching the DNA database on the relational datuhnse mcrnngement system, SYBASE, at DDBJ. The...
TACT: Transcriptome Auto-Annotation Conducting Tool of H-InvDB (2008)
Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the
Murakami, Katsuhiko, Imanishi, Tadashi, Gojobori, Takashi, Nakai, Kenta
Abstract Background It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis -elements, yet we have limited knowledge of, for example, the...
Hwang, Jung Shan, Takaku, Yasuharu, Chapman, Jarrod, Ikeo, Kazuho, David, Charles N., Gojobori, Takashi
The cnidocil at the apical end of Hydra nematocytes is a mechanosensory cilium, which acts as a “trigger” for discharge of the nematocyst capsule. The cnidocil protrudes from the center of the...
Nakagawa, So, Niimura, Yoshihito, Gojobori, Takashi, Tanaka, Hiroshi, Miura, Kin-ichiro
Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the accurate annotation of genome sequences. Kozak reported that the nucleotide sequence GCCGCC(A/G)CCAUGG (AUG...
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...
Takeda, Jun-ichi, Suzuki, Yutaka, Sakate, Ryuichi, Sato, Yoshiharu, Seki, Masahide, Irie, Takuma, ...
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants...
Structure and Developmental Expression of the Ascidian (2007)
Gene Insights Into, Shigeru Sato, Reiko Toyoda, You Katsuyama, Hidetoshi Saiga, Takaharu Numakunai, ...
The tyrosinase family in vertebrates consists of three related melanogenic enzymes: tyrosinase, tyrosinase-related protein-1 (TRP-1), and TRP-2. These proteins control melanin production in pigment...
The non-redundant Baci lus subtilis (NRSub) database: update 1998 (2007)
Guy Perrière, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome (2007)
To elucidate the evolution of mammalian genomes, it is crucial to estimate the number of genes in the genome and to measure the degree of redundancy in the genome in various species. The number of...
Hideaki Sugawara, Yoji Nakamura, Kazuho Ikeo, Satoru Miyazaki, Takashi Gojobori, Kenji Satou, ...
clustering
Keisuke Onishi, Hao Zhang, Takuro Tamura, Takashi Gojobori, Shintaroh Ueda
Genomic sequences of several animals were almost completely sequenced, and it was shown that human genome has relatively small numbers of genes. This suggests that not mere gene number but proteomic...
A Prototype of PubMed Central (2007)
Hideaki Sugawara, Takashi Gojobori, Takeshi Konno, Yasumasa Shigemoto, Masahito Yamaguchi
“PubMed Central (PMC) is the U.S. National Library of Medicine’s digital archive of life sciences journal literature. Access to PMC is free and unrestricted. ” [3]. It covers 78 journals and...
Liu, Qing-Xin, Nakashima-Kamimura, Naomi, Ikeo, Kazuho, Hirose, Susumu, Gojobori, Takashi
To elucidate the transcriptional regulation in eukaryotic genome network, it is important to understand coevolution of transcription factors, transcriptional coactivators, and TATA-box–binding...
Kosuge, Takehide, Abe, Takashi, Okido, Toshihisa, Tanaka, Naoto, Hirahata, Masaki, Maruyama, Yutaka, ...
A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB,...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates (2007)
Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, ...
Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Kuroda, Tsuyoshi, Sugano, Sumio, Gojobori, Takashi, ...
The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing (AS)...
DDBJ working on evaluation and classification of bacterial genes in INSDC (2007)
Sugawara, Hideaki, Abe, Takashi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) newly collected and released 12 927 184 entries or 13 787 688 598 bases in the period from July 2005 to June 2006. The released data contain...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
The formation mechanism of operons remains unresolved: operons may form by rearrangements within a genome or by acquisition of genes from other species, that is, horizontal gene transfer (HGT). One...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur,...
Sumio Sugano, Takashi Gojobori, Tadashi Imanishi
sequenced and manually annotated full-length cDNAs based on H-Invitational
Takehide Kosuge, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, ...
A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB,
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB (2006)
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
The Evolutionary Rate of a Protein Is Influenced by Features of the Interacting Partners (2006)
Makino, Takashi, Gojobori, Takashi
Rates of protein evolution are thought to be influenced by features of protein-protein interaction (PPI). However, the most important features of interaction for determining the evolutionary rate are...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
DDBJ in preparation for overview of research activities behind data submissions (2006)
Okubo, Kousaku, Sugawara, Hideaki, Gojobori, Takashi, Tateno, Yoshio
In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 956 826 entries or 1 741 313 111 bases. The released data include ∼90 000 ESTs and cDNAs of Macaca fascicularis, and 280...
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
The Evolutionary Rate of a Protein is Influenced by Features of the Interacting Partners (2006)
Makino, Takashi, Gojobori, Takashi
Rates of protein evolution are thought to be influenced by features of protein-protein interaction. However, the most important features of interaction for determining evolutionary rate are poorly...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
The formation mechanism of operons remains unresolved: operons may form by rearrangements within a genome or by acquisition of genes from other species, i.e., horizontal gene transfer. One hindrance...
Kosuge, Takehide, Abe, Takashi, Okido, Toshihisa, Tanaka, Naoto, Hirahata, Masaki, Maruyama, Yutaka, ...
A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB,...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
This paper was withdrawn by the authors.
Hendry Muljadi, Hideaki Takeda, Jiro Araki, Shoko Kawamoto, Satoshi Kobayashi, Sven Minoru Demiya, ...
This paper describes a Semantic MediaWiki, a MediaWiki extended to include the ideas of Semantic Web. The proposed Semantic MediaWiki works as an integrated system for content management and metadata...
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
The Origin and Evolution of Porcine Reproductive and Respiratory Syndrome Viruses (2005)
Hanada, Kousuke, Suzuki, Yoshiyuki, Nakane, Takashi, Hirose, Osamu, Gojobori, Takashi
Porcine reproductive and respiratory syndrome viruses (PRRSV) are divided into North American and European types, which show about 40% difference in their amino acid sequences. The divergence time of...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5' untranslated region (UTR) was investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes (2005)
Tanaka, Tsuyoshi, Tateno, Yoshio, Gojobori, Takashi
Vitamin B6 (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5′-phosphate (PLP; the active form of VB6) are known: the de novo...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5′-untranslated region (UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
The Origin and Evolution of Porcine Reproductive and Respiratory Syndrome Viruses (2005)
Hanada, Kousuke, Suzuki, Yoshiyuki, Nakane, Takashi, Hirose, Osamu, Gojobori, Takashi
Porcine reproductive and respiratory syndrome viruses (PRRSV) are divided into North American and European types, which show about 40% difference in their amino acid sequences. The divergence time of...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5' untranslated region (UTR) was investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
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...
The Human Anatomic Gene Expression Library (2004)
Motohiko Tanino, Marie-anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, ...
(H-ANGEL), the H-Inv integrative display of human gene expression across disparate
Novel algorithm for automated genotyping of (2004)
Toshiko Matsumoto, Wataru Yukawa, Yasuyuki Nozaki, Ryo Nakashige, Minori Shinya, Satoshi Makino, ...
microsatellites
Hanada, Kousuke, Suzuki, Yoshiyuki, Gojobori, Takashi
RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in...
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes (2004)
Tanaka, Tsuyoshi, Tateno, Yoshio, Gojobori, Takashi
Vitamin B6 (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5'-phosphate (PLP; the active form of VB6) are known: the de novo...
Ogura, Atsushi, Ikeo, Kazuho, Gojobori, Takashi
Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been...
Evolutionary Process of Amino Acid Biosynthesis in Corynebacterium at the Whole Genome Level (2004)
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
Novel algorithm for automated genotyping of microsatellites (2004)
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Hanada, Kousuke, Suzuki, Yoshiyuki, Gojobori, Takashi
RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in...
Hanada, Kousuke, Suzuki, Yoshiyuki, Gojobori, Takashi
RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in...
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes (2004)
Tanaka, Tsuyoshi, Tateno, Yoshio, Gojobori, Takashi
Vitamin B6 (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5'-phosphate (PLP; the active form of VB6) are known: the de novo...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Abstract Background Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian...
Ishibashi, Tomoko, Nakazawa, Masumi, Ono, Hiroaki, Satoh, Nori, Gojobori, Takashi, Fujiwara, Shigeki
Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome (2003)
Human Genome, Hiroaki Sakai, Kanako O. Koyanagi, Takeshi Itoh, Tadashi Imanishi, Takashi Gojobori
Introduction Processed pseudogenes are defined as those obtained by reverse transcription of messenger RNAs followed by reintegration into genomic DNA and subsequent degradation with disablements...
Search for the Evolutionary Origin of a Brain; Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
Search for the Evolutionary Origin of a Brain: Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
Niimura, Yoshihito, Terabe, Mahito, Gojobori, Takashi, Miura, Kin-ichiro
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA...
Nishio, Yousuke, Nakamura, Yoji, Kawarabayasi, Yutaka, Usuda, Yoshihiro, Kimura, Eiichiro, Sugimoto, Shinichi, ...
Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above...
Search for the Evolutionary Origin of a Brain; Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
The evolutionary position of nematodes (2002)
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Abstract Background The complete genomes of three animals have been sequenced by global research efforts: a nematode worm ( Caenorhabditis elegans ), an insect ( Drosophila melanogaster ), and a...
Iwama, Hisakazu, Gojobori, Takashi
Neurotransmitter receptors (neuroreceptors) are classified into two types, G protein–coupled receptors (GPCRs) and ligand-gated ion channels. The former occupies a small part of the large GPCR...
ADAPTSITE: detecting natural selection at single amino acid sites (2001)
Suzuki, Yoshiyuki, Gojobori, Takashi, Nei, Masatoshi
Summary: ADAPTSITE is a program package for detecting natural selection at single amino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program...
Sato, Toru, Terabe, Mahito, Watanabe, Hidemi, Gojobori, Takashi, Hori-Takemoto, Chie, Miura, Kin-ichiro
Nucleotide sequences around the boundaries of all open reading frames in the Escherichia coli whole genome were analyzed. Characteristic base biases were observed after the initiation codon and...
Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura
The codon usage in individual protein genes has been calculated using the nucleotide sequence obtained from the GenBank Genetic Sequence Database. Sum of the codon use of each organism has been also...
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams (2000)
Tateno, Yoshio, Miyazaki, Satoru, Ota, Motonori, Sugawara, Hideaki, Gojobori, Takashi
We at DDBJ (http://www.ddbj.nig.ac.jp ) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the...
Codon usage tabulated from international DNA sequence databases: status for the year 2000 (2000)
Nakamura, Yasukazu, Gojobori, Takashi, Ikemura, Toshimichi
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
DNA Data Bank of Japan at work on genome sequence data (1998)
Yoshio Tateno, Kaoru Fukami-kobayashi, Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori
We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp ) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome...
The non-redundant Bacillus subtilis (NRSub) database: update 1998 (1998)
Guy Perrière, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
DNA Data Bank of Japan at work on genome (1997)
Yoshio Tateno, Kaoru Fukami-kobayashi, Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori
We at the DNA Data Bank of Japan (DDBJ)
The NRSub database: update 1997 (1997)
Guy Perrière, Ivan Moszer, Takashi Gojobori
In the context of the international project aiming at sequencing the whole genome of Bacillus subtilis we have developed NRSub, a non-redundant database of sequences from this organism. Starting from...
Molecular Evolutionary Phylogenetic Tree Based on Minimum Description Length Principle (1995)
Fengrong Ren, Hiroshi Tanaka, Norio Fukuda, Takashi Gojobori
Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molec-ular evolutionary phylogenetic trees. In this paper, we deal with this problem from the...
NRSub: a non-redundant database for Bacillus subtilis (1995)
Guy Perrière, Ivan Moszer, Takashi Gojobori
In the context of the international project aimed at sequencing the whole genome of Bacillus subtilis we have developed a non-redundant, fully annotated database of sequences from this organism....
NRSub: a non-redundant data base for the Bacillus subtilis genome (1994)
Perrieère, Guy, Gouy, Manolo, Gojobori, Takashi
We have organized the DNA sequences of Bacillus subtilis from the EMBL collection to build the NRSub data base. This data base Is free from duplications and all detected overlapping sequences are...
Codon usage tabulated from the GenBank genetic sequence data (1992)
Wada, Ken-nosuke, Wada, Yoshiko, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data (1991)
Wada, Ken-nosuke, Wada, Yoshiko, Doi, Hirofumi, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank Genetic Sequence Data (1988)
Aota, Shin-ichi, Gojobori, Takashi, Ishibashi, Fumie, Maruyama, Takeo, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data (1986)
Maruyama, Takeo, Gojobori, Takashi, Aota, Shin-ichi, Ikemura, Toshimichi
Yamaguchi, Yumi, Gojobori, Takashi
Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the...
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
Tateno, Yoshio, Miyazaki, Satoru, Ota, Motonori, Sugawara, Hideaki, Gojobori, Takashi
We at DDBJ (http://www.ddbj.nig.ac.jp ) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration...
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Nakamura, Yasukazu, Gojobori, Takashi, Ikemura, Toshimichi
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Yamaguchi-Kabata, Yumi, Gojobori, Takashi
To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of...
In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence
Niimura, Yoshihito, Gojobori, Takashi
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several...
Akashi, Hiroshi, Gojobori, Takashi
Biosynthesis of an Escherichia coli cell, with organic compounds as sources of energy and carbon, requires approximately 20 to 60 billion high-energy phosphate bonds [Stouthamer, A. H. (1973) Antonie...
Tanaka, Yasuhito, Hanada, Kousuke, Mizokami, Masashi, Yeo, Anthony E. T., Shih, J. Wai-Kuo, Gojobori, Takashi, ...
The prevalence of hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) is considerably lower in the U.S. than in Japan. To elucidate this difference, we determined the time origin of the...
Mineta, Katsuhiko, Nakazawa, Masumi, Cebrià, Francesc, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Niimura, Yoshihito, Terabe, Mahito, Gojobori, Takashi, Miura, Kin-ichiro
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA...
Gaudieri, Silvana, Dawkins, Roger L., Habara, Kaori, Kulski, Jerzy K., Gojobori, Takashi
The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Doi, Hirofumi, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Aota, Shin-ichi, Tsuchiya, Rye, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank Genetic Sequence Data
Aota, Shin-ichi, Gojobori, Takashi, Ishibashi, Fumie, Maruyama, Takeo, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Maruyama, Takeo, Gojobori, Takashi, Aota, Shin-ichi, Ikemura, Toshimichi
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...
Nishio, Yousuke, Nakamura, Yoji, Kawarabayasi, Yutaka, Usuda, Yoshihiro, Kimura, Eiichiro, Sugimoto, Shinichi, ...
Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above...
Ogura, Atsushi, Ikeo, Kazuho, Gojobori, Takashi
Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been...
Iwama, Hisakazu, Gojobori, Takashi
Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the...
Novel algorithm for automated genotyping of microsatellites
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
DDBJ in preparation for overview of research activities behind data submissions
Okubo, Kousaku, Sugawara, Hideaki, Gojobori, Takashi, Tateno, Yoshio
In the past year, DDBJ () collected and released 1 956 826 entries or 1 741 313 111 bases. The released data include ∼90 000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
Codon Substitution in Evolution and the "Saturation" of Synonymous Changes
A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61 x 61...
Andrews, T Daniel, Gojobori, Takashi
The PilE protein is the major component of the Neisseria meningitidis pilus, which is encoded by the pilE/pilS locus that includes an expressed gene and eight homologous silent fragments. The silent...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Shiina, Takashi, Ota, Masao, Shimizu, Sayoko, Katsuyama, Yoshihiko, Hashimoto, Nami, Takasu, Miwa, ...
A plausible explanation for many MHC-linked diseases is lacking. Sequencing of the MHC class I region (coding units or full contigs) in several human and nonhuman primate haplotypes allowed an...
A C + + computational environment for biomolecular sequence management
M. Chiusano, Takashi Gojobori, G. Toraldo
The wide production of biomolecular data of the last 30 years, mainly due to the rapid evolving of technologies as well as to the accomplishment of the Genome Projects, led to the necessity of...
Yamaguchi, Yumi, Gojobori, Takashi
Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the...
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
Tateno, Yoshio, Miyazaki, Satoru, Ota, Motonori, Sugawara, Hideaki, Gojobori, Takashi
We at DDBJ (http://www.ddbj.nig.ac.jp ) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration...
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Nakamura, Yasukazu, Gojobori, Takashi, Ikemura, Toshimichi
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Yamaguchi-Kabata, Yumi, Gojobori, Takashi
To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of...
In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence
Niimura, Yoshihito, Gojobori, Takashi
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several...
Akashi, Hiroshi, Gojobori, Takashi
Biosynthesis of an Escherichia coli cell, with organic compounds as sources of energy and carbon, requires approximately 20 to 60 billion high-energy phosphate bonds [Stouthamer, A. H. (1973) Antonie...
Tanaka, Yasuhito, Hanada, Kousuke, Mizokami, Masashi, Yeo, Anthony E. T., Shih, J. Wai-Kuo, Gojobori, Takashi, ...
The prevalence of hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) is considerably lower in the U.S. than in Japan. To elucidate this difference, we determined the time origin of the...
Mineta, Katsuhiko, Nakazawa, Masumi, Cebrià, Francesc, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Niimura, Yoshihito, Terabe, Mahito, Gojobori, Takashi, Miura, Kin-ichiro
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA...
Gaudieri, Silvana, Dawkins, Roger L., Habara, Kaori, Kulski, Jerzy K., Gojobori, Takashi
The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Doi, Hirofumi, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Aota, Shin-ichi, Tsuchiya, Rye, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank Genetic Sequence Data
Aota, Shin-ichi, Gojobori, Takashi, Ishibashi, Fumie, Maruyama, Takeo, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Maruyama, Takeo, Gojobori, Takashi, Aota, Shin-ichi, Ikemura, Toshimichi
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...
Nishio, Yousuke, Nakamura, Yoji, Kawarabayasi, Yutaka, Usuda, Yoshihiro, Kimura, Eiichiro, Sugimoto, Shinichi, ...
Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above...
Ogura, Atsushi, Ikeo, Kazuho, Gojobori, Takashi
Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been...
Iwama, Hisakazu, Gojobori, Takashi
Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the...
Novel algorithm for automated genotyping of microsatellites
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
Codon Substitution in Evolution and the "Saturation" of Synonymous Changes
A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61 x 61...
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
DDBJ in preparation for overview of research activities behind data submissions
Okubo, Kousaku, Sugawara, Hideaki, Gojobori, Takashi, Tateno, Yoshio
In the past year, DDBJ () collected and released 1 956 826 entries or 1 741 313 111 bases. The released data include ∼90 000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse...
Andrews, T Daniel, Gojobori, Takashi
The PilE protein is the major component of the Neisseria meningitidis pilus, which is encoded by the pilE/pilS locus that includes an expressed gene and eight homologous silent fragments. The silent...
Shiina, Takashi, Ota, Masao, Shimizu, Sayoko, Katsuyama, Yoshihiko, Hashimoto, Nami, Takasu, Miwa, ...
A plausible explanation for many MHC-linked diseases is lacking. Sequencing of the MHC class I region (coding units or full contigs) in several human and nonhuman primate haplotypes allowed an...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates
Wang, Hurng-Yi, Chien, Huan-Chieh, Osada, Naoki, Hashimoto, Katsuyuki, Sugano, Sumio, Gojobori, Takashi, ...
Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their...
DDBJ working on evaluation and classification of bacterial genes in INSDC
Sugawara, Hideaki, Abe, Takashi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) () newly collected and released 12 927 184 entries or 13 787 688 598 bases in the period from July 2005 to June 2006. The released data contain honeybee expressed...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Kuroda, Tsuyoshi, Sugano, Sumio, Gojobori, Takashi, ...
The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing (AS)...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice
Osato, Naoki, Suzuki, Yoshiyuki, Ikeo, Kazuho, Gojobori, Takashi
For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands...
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...
Nakagawa, So, Niimura, Yoshihito, Gojobori, Takashi, Tanaka, Hiroshi, Miura, Kin-ichiro
Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the accurate annotation of genome sequences. Kozak reported that the nucleotide sequence GCCGCC(A/G)CCAUGG (AUG...
Hwang, Jung Shan, Ohyanagi, Hajime, Hayakawa, Shiho, Osato, Naoki, Nishimiya-Fujisawa, Chiemi, Ikeo, Kazuho, ...
Cell lineages of cnidarians including Hydra represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal...
Distribution and Effects of Nonsense Polymorphisms in Human Genes
Yamaguchi-Kabata, Yumi, Shimada, Makoto K., Hayakawa, Yosuke, Minoshima, Shinsei, Chakraborty, Ranajit, Gojobori, Takashi, ...
Takeda, Jun-ichi, Suzuki, Yutaka, Sakate, Ryuichi, Sato, Yoshiharu, Seki, Masahide, Irie, Takuma, ...
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants...
Codon usage tabulated from the international DNA sequence databases
Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura
CUTG (codon usage tabulated from GenBank) is a comprehensive database for codon usage. The codon usage for each full-length protein gene has been calculated using the nucleotide sequence obtained...
Detecting Linkage between a Trait and a Marker in a Random Mating Population without Pedigree Record
Mano, Shuhei, Endo, Takaho A., Oka, Akira, Ozawa, Akira, Gojobori, Takashi, Inoko, Hidetoshi
Modern linkage-based approaches employing extended pedigrees are becoming powerful tools for localizing complex quantitative trait loci. For these linkage mapping methods, it is necessary to...
Optimized ancestral state reconstruction using Sankoff parsimony
Clemente, José C, Ikeo, Kazuho, Valiente, Gabriel, Gojobori, Takashi
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts
Shimada, Makoto K., Matsumoto, Ryuzou, Hayakawa, Yosuke, Sanbonmatsu, Ryoko, Gough, Craig, Yamaguchi-Kabata, Yumi, ...
Creation of a vast variety of proteins is accomplished by genetic variation and a variety of alternative splicing transcripts. Currently, however, the abundant available data on genetic variation and...
DDBJ dealing with mass data produced by the second generation sequencer
Sugawara, Hideaki, Ikeo, Kazuho, Fukuchi, Satoshi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period...
Fukuchi, Satoshi, Homma, Keiichi, Sakamoto, Shigetaka, Sugawara, Hideaki, Tateno, Yoshio, Gojobori, Takashi, ...
The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and...
Midline governs axon pathfinding by coordinating expression of two major guidance systems
Liu, Qing-Xin, Hiramoto, Masaki, Ueda, Hitoshi, Gojobori, Takashi, Hiromi, Yasushi, Hirose, Susumu
Formation of the neural network requires concerted action of multiple axon guidance systems. How neurons orchestrate expression of multiple guidance genes is poorly understood. Here, we show that...