DNA Data Bank of Japan Center for Information Biology National Institute of Genetics

DDBJ/CIB Report

CIB Research Report 2001 Published by the Center for Information Biology, National Institute of Genetics Mishima, Japan Vol. 4 March 2001

Contents 1. News from CIB --------------------------------------2. Research Activities in CIB -------------------------2.1 Laboratory for DNA Data Analysis ------------2.2 Laboratory for Gene Function Research ------2.3 Laboratory for Gene-Product Informatics ----2.4 Laboratory for Molecular Classification ------3. CIB Staff Publications ------------------------------4. CIB Research Staff ----------------------------------

27 29 29 32 33 33 36 37

1. News from CIB Publication of human genome draft sequences Article on human genome draft sequences was published in Nature, February 15 (vol. 409, pp. 860-921) by International Human Genome Sequencing Consortium. Public research institutions in USA, United Kingdom, Japan, France, Germany, and China consist of this international Consortium. Human Genome Research Group at RIKEN Genomic Sciences Center (Project Director: Sakaki Yoshiyuki) and research group of Professor Shimizu Nobuyoshi at Department of Molecular Biology, Keio University School of Medicine are involved in this International Consortium from Japan. GenBank/NCBI, EMBL/EBI, and DDBJ/CIB, which are constructing and maintaining nucleotide sequence database through international collaboration, were also mentioned at the end of this paper. - CIB Research Report 2001 -

27

Announcement was made in last June at White House on the completion of this human genome draft sequences, followed by improvement of sequence quality and biological analyses. All the efforts produced Nature paper and Science paper by Celera Genomics. As written at the beginning of Nature paper, 100 years after the rediscovery of Mendel's laws of heredity, we human beings reached the fundamental level of our own genetic information in which no further details cannot be described. This achievement also has a great significance as the starting point of Biology in the 21st Century. International Human Genome Sequencing Consortium had simultaneous press releases worldwide prior publication of Nature paper on February 12. In Japan, director Wada Akiyoshi, project director Sakaki Yoshiyuki, and team leader Fujiyama Asao of RIKEN Genomic Sciences Center, professor Shimizu Nobuyoshi and associate professor Minoshima Nobuo of Keio University School of Medicine, and professor Sugawara Hideaki of Center for Information Biology, National Institute of Genetics attended the press release. Professor Sugawara represented DNA Data Bank of Japan (DDBJ), and Dr. Fujiyama is at Department of Human Genetics, National Institute of Genetics. Following results through genomic analyses (from Nature paper) enhance our intellectual curiosity such as evolution of our own species, variety of humanbiological phenomena.

● The genomic landscape shows marked variation in the distribution of a number of features, including genes, transposable elements, GC content, CpG islands and recombination rate. This gives us important clues about function. For example, the developmentally important HOX gene clusters are the most repeat-poor regions of the human genome, probably reflecting the very complex coordinate regulation of the genes in the clusters. ● There appear to be about 30,000 to 40,000 protein-coding genes in the human genomeonly about twice as many as in worm or fruit fly. However, the genes are more complex, with more alternative splicing generating a larger number of protein products. ● The full set of proteins (the `proteome') encoded by the human genome is more complex than those of invertebrates. This is due in part to the presence of vertebratespecific protein domains and motifs (an estimated 7% of the total), but more to the fact that vertebrates appear to have arranged pre-existing components into a richer collection of domain architectures. ● Hundreds of human genes appear likely to have resulted from horizontal transfer from bacteria at some point in the vertebrate lineage. ● Although about half of the human genome derives from transposable elements, there has been a marked decline in the overall activity of such elements in the hominid lineage. DNA transposons appear to have become completely inactive and long-terminal repeat (LTR) retroposons may also have done so. ● The mutation rate is about twice as high in male as in female meiosis. ● Recombination rates tend to be much higher in distal regions of chromosomes and on shorter chromosome arms in general, in a pattern that promotes the occurrence of at least one crossover per chromosome arm in each meiosis. ● More than 1.4 million single nucleotide polymorphisms (SNPs) in the human genome have been identified.

28

- CIB Research Report 2001 -

All nucleotide sequence data determined by International Human Genome Sequencing Consortium are open from DDBJ/EMBL/GenBank International Nucleotide Sequence Database. We DDBJ show those sequence entries either in HTG or HUM division of the DDBJ database. Chromosome-wise human sequence data can be retrieved from downloading site of the DDBJ/CIB Human Genomics Studio. Nucleotide sequence data released by International Human Genome Sequencing Consortium and those determined by Celera Genomics differ. For example, International Consortium covered human genome by small number of long contigs, while Celera did by many short contigs. Results of sequence analyses also differ, probably caused by use of different material (individual difference), by difference on nucleotide sequence determination and way of data analyses. However, data produced by Celera Genomics are not released through public databases, but from the company server with usage limitation. Many protests, including that by Science Council of Japan, were made againt this situation, because this kind of activity may cause loss of reproducibility that must be assured in scientific papers, and because this will lead to fragmentation of database important for biological studies. Although such political issues remain, when the whole nucleotide sequences of the human genome is obtained within 2-3 years, this will become a great achievement not only of biology but of modern civilization. We, DNA Data Bank of Japan (DDBJ), have an important responsibility to construct database in this international enterprise, and will expand our efforts. We expect your continuous cooperation. CIB to be renamed CIB/DDBJ The Center for Information Biology (CIB) of the National Institute of Genetics (NIG) will change its name to "the Center for Information Biology and DNA Data Bank of Japan (CIB/DDBJ)" since April 2001. Since DDBJ began its operations in 1986, it has been regarded as a project of the DNA Research Center and then as a project of CIB. Now DDBJ will be officially recognized as an organization of NIG. We at CIB believe that this is because of the increasing importance of information biology and biological databases in life sciences today, especially in the field of genome science. Therefore, we should be more responsible for our research and database activities than ever. Through these activities, the new Center will continue to contribute to the development of information biology and related areas worldwide.

2. Research Activities in CIB 2.1 Laboratory for DNA Data Analysis Prof. Takashi Gojobori Assist. Prof. Kazuho Ikeo Assist. Prof. Tadashi Imanishi The laboratory for DNA Data Analysis is currently composed of three faculty members (above), 11 postdoctoral research fellows (including one studying in the USA), four visiting researchers, six graduate students, eight technical and research assistants, and seven supporting staff. In total, there are 39 people in our laboratory. Furthermore, a number of new postdocs and a new graduate student are expected to join our laboratory this year. All staff members are engaged in research projects in this laboratory. Three faculty staff and six supporting staff are also involved in DDBJ activities. - CIB Research Report 2001 -

29

We are pursuing three major research interests: (1) The evolution of nervous system, especially brain and eye, (2) the molecular evolution of genomes, and (3) basic molecular evolutionary research. The area of first interest is mostly experimental, and includes subjects such as gene expression profiling of the planarian brain by EST sequencing and DNA chip experiments. The second interest, genomic evolution, involves solely computational work and includes topics such as analysis of base composition and gene density in the human genome, evolution of duplicated chromosomal regions, and the detection of horizontal gene transfer. Our third research interest includes theoretical and analytic studies of basic process of molecular and organismal evolution. Although these three subject areas seem disparate, all aim at elucidating the evolution of genes and organisms, which has been and still is the persistent theme of study in our laboratory. Current topics of research projects in this laboratory are: Gene expression profiling of planarian brains based on EST sequencing and DNA chip technology Phylogenetic studies of fish species based on mitochondrial DNA sequences Evolution of pathogenic viruses such as HIV, and the influenza and hepatitis viruses Molecular evolution of the homeobox gene family (K. Ikeo) Designing a 3D image database (bio-simulator database) of developmental processes (K. Ikeo) Molecular evolution of duplicated chromosomal regions within eukaryotic genomes (T. Imanishi) Prediction of deleterious mutations that might occur in the human genome (T. Imanishi) Base compositional localisation of genes in the human genome sequence (D. Andrews) Analysis of adaptive molecular evolution in complete genome sequences (D. Andrews) Higher evolutionary rates in the contact regions between catecholamine receptors and G proteins (H. Iwama)

In silico reconstruction of Giemsa banding patterns from the human genome sequence (Y. Niimura) Construction of a microsatellite database from the human genome sequence (T. A. Endo) SNP profiles of human subgenomic regions (M. Ogasawara) Survey of brain-specific genes by use of a planarian cDNA chip (M. Nakazawa) Role of apoptosis in the regeneration of planarians (JS. Hwang) Molecular evolution of the vsx gene family (Y. Uchiyama) The history of domestication

of chickens, viewed using genetic and cultural information (T. Komiyama)

Evolution of sex chromosomes in teleosts (K. Ota) Evolutionary features of the gene expression profile from the planarian brain (K. Mineta) Molecular evolution of the porcine reproductive and respiratory syndrome virus (PRRSV) (K. Hanada) Detection of horizontal gene transfer among microbial genomes (Y. Nakamura) Analysis of the evolution of the eye and nervous system using comparative analysis of EST and genomic sequence information (A. Ogura)

Below we present some of our research topics in detail. Please visit our homepage (http:/ /www.cib.nig.ac.jp/dda/home.html) for more information. (1) Evolutionary features of the gene expression profile of planarian brain (K. Mineta) The planarian possesses one of the more primitive central nervous system (CNS) yet discovered, and hence the planarian is a useful model for understanding evolutionary processes that may have formed the CNS. Our purpose has been to identify planarian genes related to the CNS, to observe their expression profiles, and to compare these with those of other species. We have sequenced over 8,000 redundant EST (Expressed Sequence Tag) clones from a cDNA library derived from the head portion of the planarian (Dugesia japonica). As a result, we have obtained a total of 3,100 non-redundant EST clones. According to a frequency analysis, 77% of these 3,100 clones are unique, and implies that most of the genes are expressed only at low levels. Conducting homology searches, we found that 44% of the 3,100 clones had significant similarities with proteins whose functions were known. Among these genes, we found that at least 71 genes were involved 30

- CIB Research Report 2001 -

in CNS-related processes. One of the 71 genes was the synaptotagmin (Djsyt) gene that is known to have an expression pattern specific to neurons determined by whole-mount in situ hybridization (Tazaki et al. BBRC 260: 426-432, 1999). Comparing these 71 planarian genes with genes from human, mouse, fruit fry and nematode, we found that 68 genes were well-conserved and that only three genes were poorly conserved. This feature can be considered as a reflection of the diversification of the CNS during evolution, supporting our idea that a comparative analysis using planarian ESTs will aid the understanding of the evolutionary processes that have created the CNS. (2) The base compositional localisation of genes in the human genome sequence (D. Andrews) We have analysed the distribution of genes within the finished portion of the human genome sequence to look for correlations between the presence of genes and the base composition of the isochore in which they reside. A window analysis was employed to divide the approximately 650Mb of finished non-redundant human genome sequence into contiguous 100Kb regions in which base composition was calculated. A new partial annotation method that uses non-redundant EST or cDNA sequence information was then applied to gain relative measures of the density of coding sequences within each window. Hence, the relationship between gene density and isochore base composition was directly appraised. Previous studies have found high concentrations of genes in the highest G+C regions of the human genome, but we have found that the gene distribution is actually far more uniform. While genes are rare in the most A+T rich regions of the genome, there is comparatively less than a four-fold enrichment of genes in the G+C richest isochores. Our findings predict that only around 26% of all genes are to be found in the approximately 12% of the human genome that represents the highest G+C isochore families. These results are supported by the recently published full draft of the human genome sequence obtained by the public genome sequencing effort, and by the sequence analysis conducted by Celera Genomics. These findings have strong implications for our current understanding of the processes of isochore formation in warm-blooded vertebrates. (3) Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome b genes (by Akihito, A. Iwata, T. Kobayashi, K. Ikeo, T. Imanishi, H. Ono, Y. Umehara, C. Hamamatsu, K. Sugiyama, Y. Ikeda, K. Sakamoto, Akishinonomiya Fumihito, S. Ohno, and T. Gojobori; published in Gene 259:5-15, 2000) The Gobioidei is a large suborder in the order Perciformes that consists of more than 2000 species belonging to about 270 genera. The sheer number of species, and the diverse morphological and behavioral specializations displayed by this suborder makes classification of the gobioid fishes very difficult. A comprehensive estimation of the evolutionary history of all gobioid species using only morphological information is difficult for two major reasons. First, in addition to wide ecological diversification, there is a trend towards specialization and degeneration of morphological characters among these species. Second, an appropriate outgroup for the gobioid fishes has not been identified. Based upon nucleotide sequence comparisons of the mitochondrial cytochrome b gene from a range of gobioid fishes, we have established the phylogenetic relationships that define their differentiation into many groups of morphological and ecological diversity. The phylogenetic trees obtained show that most of the species examined have diverged from each other almost simultaneously, or at least have diverged during an extremely short period of time. (T. Imanishi)

- CIB Research Report 2001 -

31

2.2 Laboratory for Gene Function Research Prof. Yoshio Tateno Assist. Prof. Kaoru Fukami-Kobayashi The members of the laboratory are: Dr. Yoshio Tateno (Professor), Dr. Kaoru FukamiKobayashi (Assistant Professor) and Ms. Mieko Hirashima (Secretary). We mainly aim at the elucidation of the origin, evolution and function of genes and proteins in view of molecular evolution, structural biology and information biology. In addition to the research activities described below, we take part in DDBJ activities. (1) Evolution of the HLA class I region in human genome HLA class I region is occupied mainly by A, B and C loci, where B and C loci are located in duplicated genome fragments respectively. We found several defective LINE sequences in both fragments, and found that they were homologous between the fragments. We estimated the evolutionary origin of B and C loci by analyzing the LINE sequences. It is known that these loci have a great number of alleles. Investigation into their origin led us to the suggestion that some of them originated from a common ancestor of human and chimpanzee, supporting the trans-species polymorphism that J. Klein has proposed. This would be an interesting case where neutral LINE sequences and a gene being subject to typical positive selection co-exist and co-evolve in a unit genome fragment. This work was carried out in collaboration with Dr. H. Inoko of Tokai University and Dr. M. Yamazaki of Fujiya Bioscience Institute. (2) Evolution of protein structure in the periplasmic binding protein (PLBP) superfamily In the previous study (Fukami-Kobayashi et al, 1999), we have shown that one of the type I PLBPs is most likely to resemble a primordial PLBP, and that a type II PLBP arose from the type I PLBPs to evolve into various type II PLBPs. Recently, the crystal structures of another type of PLBPs have been reported. The topological arrangements of the type III PLBPs are different from either type. To find a clue to the evolutionary origin of the type III, we constructed phylogenetic trees for PLBPs and their partner ABC proteins, and obtained a preliminary result that the type III was closer to the type II. Some of bacterial transcription factors such as lactose repressor (LacI) and purine repressor (PurR) are homologous to periplasmic binding proteins (PLBPs) in their C-terminal ligand binding domains. Phylogenetic analysis of repressors and their PLBP homologues revealed that the attachment of the DNA-binding domain was originated first, and substrate specificity was gained in evolution thereafter. The tree also shows that the emergence of the attachment predates the divergence of major lineages of eubacteria. This work is being carried out in collaboration with Dr. K. Nishikawa of CIB. (3)Compensatory covariation in protein evolution Compensatory covariation arises in divergent evolution of protein sequences, when two amino acid sites have particular mutations that work together to maintain a global property of a protein (net charge, for example), while each mutation alone does not. We are now finding such covariations by examining branches of an evolutionary tree of a specified group of proteins and reconstructing ancestral sequences in it. This work is an outcome of the collaboration with Dr. S. A. Benner of Florida University. (Y. Tateno and K. Fukami-Kobayashi)

32

- CIB Research Report 2001 -

2.3 Laboratory for Gene-Product Informatics Prof. Ken Nishikawa Assist. Prof. Motonori Ota The Nishikawa laboratory now consists of 14 members: Professor Nishikawa, Assist. Professor Ota, three post-doctoral research fellows (Drs. Kawabata, Fukuchi and Homma), two graduate students (Messrs. Kinjo and Kashiwagi), five technical assistants (Mses. Mimura, Yamamoto, Kuromaru, Abe, Suzuki and Ito) and a secretary (Ms. Narita). Recently we are addressing so-called “structural genomics”, which investigates protein structure in terms of genomes. More than 20 completely sequenced genomes have been computationally analyzed in terms of protein structure and functions. The resulting database “GTOP” has been made publicly available through the WWW (http://spock.genes.nig.ac.jp/~genome/ gtop.html). To promote structural genomics in Japan, we successfully co-organized a workshop on computational genomics in Tokyo last January, aided by a grant-in-aid from the Ministry of Education, Culture, Sports, Science and Technology. Some pictures of this workshop can be viewed at http://spock.genes.nig.ac.jp/koji-genome/Wsphoto.html. Moreover, we have investigated methodologies of protein structure comparison and protein structure prediction, protein folding energetics, di-nucleotide or amino acid composition analysis of complete genomes, the origin of the thermal stability of thermophile proteins, and de novo protein designs. We also have constructed the Protein Mutant Database (PMD). (M. Ota)

2.4 Laboratory for Molecular Classification Prof. Hideaki Sugawara Assist. Prof. Satoru Miyazaki (1) Research and Development for DDBJ 1) From YAMATOII to TSUNAMI The laboratory is in charge of the development and management of databases for DDBJ. Since 1998, DDBJ has developed a data submission system with parser in order to process massive data originated from genome projects and a study on biodiversity. The development was in time for the completion of the draft sequencing of human genome in June 2000. In the meantime, the system could also cope with a number of cDNA sequences of mice. DDBJ expects that the draft sequences will be updated, especially by improvement of annotation. It requires streamline of the system for review and release of data. Therefore, DDBJ looked through the existing microbial genome data into GIB whenever genome sequencing were completed and the data is made open to the publ review system (YAMATOII) and the mass submission system resulting in planning a new data processing system. Development of the new system is named TSUNAMI project and is underway. 2) Expansion of Genome Information Broker (GIB) GIB was originally created for E. coli genome for the retrieval and analysis of genomic information in a set. We implemented ic. At the GIB Web page(http://www.ddbj.nig.ac.jp/), key - CIB Research Report 2001 -

33

word search, homology search, links to KEGG and GTOP and visualization of the data are available for 42 organisms as of February 2001. We plan to implement results of comparative genomics and also utilize XML, CORBA and distributed databases as shown in Fig. 1. Fig 1. XML and CORBA in GIB

Server ○ ○

CORBA

○

○

○

Analyze FORM Create query XML

○

○

Client

○ ○

○

○

○

○

Analyze query XML Carry out query

○

Produce results in XML

○

Analyze results in XML Create HTML

○

CORBA

{

Key word search Homology search

Reference: Journal of Japan Society of Information and Knowledge, Vol. 10, No.4 , pp.4-13 (2001) 3) Application of XML to DDBJ Interoperability of databases is still an issue in bioinformatics. XML is a powerful yet simple tool that may improve the interoperability. We defined a data type definition (DTD) for DDBJ entries. The XML will firstly be implanted into the DDBJ retrieval system “getentry”. It will make it possible to integrate automatically a private database and a subset of DDBJ based on DTD. Reference: Genome Informatics 11:380-381 (2000) (2) Research and Development for WFCC-MIRCEN World Data Centre for Microorganisms (WDCM) 1)WDCM WFCC and MIRCEN stand for World Federation for Culture Collections and Microbial Resource Centers network respectively. The laboratory is a host of WDCM that is the data center of WFCC and MIRCEN. We maintain the world directory of 500 culture collections in 60 countries in databases of “CCINFO” and “STRAIN” that are accessible at http://wdcm.nig.ac.jp/. 2) Development of a Workbench for Biological Classification and Identification (InforBIO) We have been interested in introduction and development new Internet technologies. We introduced the World Wide Web (WWW) as one of the first ten WWW servers. We also developed a simultaneous search system of distributed system named Agent for Hunting Microbial Informa34

- CIB Research Report 2001 -

tion in Internet (AHMMI). We now develop the digital workbench named InforBIO. In InforBIO, users are able to integrate databases and analytical tools that are distributed in the Internet including their own resources. We aim at an open system by use of JAVA, XML, and tools of CORBA and a relational database management system in the public domain. We will distribute the prototype of InforBIO in CD-ROM this year. (3) Others 1) Data processing system for patent sequences DDBJ has received patent sequences from Japan Patent Office (JPO) and disseminate them to the public. Therefore DDBJ and JPO have discussed about a system for data transfer from JPO to DDBJ. This year, we cooperated a survey by Japan Bioindustry Association (JBA) on data processing system in European Patent Office (EPO) and United States Trademark and Patent Office (USTPO). It is to be noted that EPO has already uses the EMBL data system that is outside EPO. USTPO also look into the possibility to use computer resources outside. The primary reason of the outsourcing is to realize efficient data processing while sequence data increase exponentially. 2) Biological Resources Centres (BRC) The Working Party for Biotechnology (WPB) of OECD set up a task force on BRC in February1999 to develop a policy guidance to support BRCs. Professor Hideaki Sugawara is the chair of the task force and compiled a report entitled “Biological Resource Centres: Underpinning the future of life sciences and biotechnology”. The report calls for actions in OECD countries and beyond. The report and a follow-up task force were approved by WPB on 16 February 2001. 3) Global Biodiversity Information Facility (GBIF) GBIF is a scheme that was created by a Biological Informatics working group in Megascience Forum of OECD. GBIF will improve the accessibility of all kinds of data of all kinds of organisms on the globe. One of the staffs (HS) participated in the discussion of the working group for three years and it is expected that the laboratory will contribute GBIF when it becomes reality. The GBIF HomePage is at http://www.gbif.org/. (H. Sugawara)

- CIB Research Report 2001 -

35

3. CIB Staff Publications in 2000-2001 (as of March 2001) Abola E E , Bairoch A, Baker W C, Beck S, Benson D A, Berman H, Cameron G, Cantor C, Doubet S, Hubbbard T J P, Jones T A, Kleywegt G J, Kolaskar A S, Kuik Van A, Lesk A M, Mews HW, Neuhaus D, Pfeiffer F, TenEyck L F, Simpson R J, Stosser G, Sussman J L, Tateno Y, Tsugita H, Ulrich E L and Viegenthart J F G. Quality control in data banks for molecular biology. BioEssays. (2000) 22: 1024-1034. Akihito, Iwata A, Kobayashi T, Ikeo K, Imanishi T, Ono H, Umehara Y, Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K., Fumihito A, Ohno S and Gojobori T. Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome b genes. GENE. (2000) 259 (1-2): 5-15. Gaudieri S, Dawkins R L, Habara K, Kulski J K and Gojobori T. SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity. Genome Research. (2000) 10 (10): 1579-1586. Gojobori T. Susumu Ohno 1928-2000. GENE. (2000) 259(1-2): 2-3. Goto K, Miyazaki S, and Sugawara H. Genome Information Broker for Data Retrieval and Comparative Analysis of Microbial Genomes. Jounal of Japan Society of Information and Knowledge. (2001) 10 (4): 4-13. Isogai Y, Ishii A, Fujisawa T, Ota M and Nishikawa K. Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties. Biochemistry. (2000) 39: 5683-5690. Isogai Y, Ishii A, Ishida M, Mukai M, Ota M, Nishikawa K and Iizuka T. Structural and functional properties of designed globins. Proc. Indian Acad. Sci (Chem. Sci.). (2000) 112: 215-221. Kawabata T and Nishikawa K. Protein tertiary structure comparison using the Markov transition model of evolution. Proteins. (2000) 41: 108-122. Kawabata T, Arisaka F and Nishikawa K. Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches. Genes. (2000) 259: 223-233. Kinjo A R, Kidera A, Nakamura H and Nishikawa K. Physicochemical evaluation of protein folds predicted by threading. Eur. Biophys. J. (in press). Miyazaki S, Hashimoto H, Shimada A, Tateno Y and Sugawara H. A new file format and tools for the large-scale data submission to DNA Data Bank of Japan (DDBJ). In Currents in Computational Molecular Biology.(2000) 60-61. Miyano S, Shamir R and Takagi T ed., Universal Academy Press, Tokyo. Nakane S, Shirabe S, Moriuchi R, Mizokami A, Furuya T, Nishiura Y, Okazaki S, Nakamura N, Suzuki Y, Nakamura T, Katamine S and Gojobori T. Comparative molecular analysis of HTLV-I proviral DNA in HTLV-I infected members of a family with a discordant HTLV-I associated myelopathy in monozygotic twins. Journal of Neuro Virology. (2000) 6: 275-283. Nakashima H and Nishikawa K. The genomic DNA sequences of various species are distinctively distributed in nucleotide compostion space. Res. Comm. In Biochem. Cell & Mol. Biol. (2000) 4: 25-45. Ota K, Kobayashi T, Ueno K and Gojobori T. Evolution of heteromorphic sex chromosomes in the order Aulopiformes. GENE (2000) 259(1-2): 25-30. Pineda D, Gonzalez J, Callaerts P, Ikeo K, Gehring W J and Salo E. Searching for the prototypic eye genetic network: Sine oculis is essential for eye regeneration in planarians. Proc Natl Acad Sci U S A. (2000) 25;97(9): 4525-9. RIKEN Genome Exploration Research Group Phase II Team and FANTOM Consortium (Okazaki Y, Gojobori T, et al.). Genelal organizer: Hayashizaki Y. Functional anotation of a fulllength mouse cDNA collection. Nature. (2001) 409; 6821: 685-690. Seki M, Higashiyama Y, Mizokami A, Kadota J I, Moriuchi R, Kohno S, Suziki Y, Takahashi K,

36

- CIB Research Report 2001 -

Gojobori T and Katamine S. Up-regulation of human T lymphotropic virus type 1 (HTLV-1) tax/rex mRNA in infected lung tissues. Clin Exp Immunol.(2000) 120: 488-498. Shimizu N and Gojobori T. How can human and simian immunodeficiency viruses utilize chemokine receptors as their coreceptors? GENE. (2000) 259(1-2): 199-205. Sugawara H and Miyazaki S. A workbench for the research and development of biological diversity. Currents in Computational Molecular Biology. (2000) 58-59. Miyano S and Takagi T ed., Universal Academy Press, Tokyo. Suzuki Y, Yamaguchi-Kabata Y and Gojobori T. Nucleotide substitution rates of HIV-1. AIDS Reviews. (2000) 2(1): 39-47. Tateno Y, Miyazaki S, Ota M, Sugawara H and Gojobori T. DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. (2000) 28: 24-26. Toyoda R, Sato S, Ikeo k, Gojobori T, Numakunai T, Goding C R and Yamamoto H. Pigment cellspecific expression of the tyrosinase gene in ascidians has a different regulatory mechanism from vertebrates. GENE. (2000) 259(1-2): 159-170. Yamaguchi-Kabata Y and Gojobori T. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J.Virology. (2000) 74(9): 4335-4350. Yusuf A M, Khan M L A, Shakir M A, Fukami-Kobayashi K, Nishikawa K and Sidduqui S S. Expression and cDNA cloning of klp-12 gene encoding an ortholog of the chichen chromokinesin, mediatingchromosome segregation in Caenorhabditis elegans. J. Biochem. Mol. Biol. (2000) 33: 138-146. *Some of the publications in Japanese were excluded. See our homepage for details.

4. CIB Research Staff Takashi Gojobori, Director and Professor ([email protected]) Kazuho Ikeo, Assistant Professor ([email protected]) Tadashi Imanishi, Assistant Professor ([email protected]) Yoshio Tateno, Professor ([email protected]) Kaoru Fukami-Kobayashi, Assistant Professor ([email protected]) Ken Nishikawa, Professor ([email protected]) Motonori Ota, Assistant Professor ([email protected]) Hideaki Sugawara, Professor ([email protected]) Satoru Miyazaki, Assistant Professor ([email protected])

- CIB Research Report 2001 -

37

CIB Research Report, Vol. 4. March 2001 Center for Information Biology National Institute of Genetics Yata 1-111, Mishima, Shizuoka 411-8540, Japan Fax: +81-559-81-6848 Home Page: http://www.cib.nig.ac.jp/ Editorial Staff:

38

Kaoru Fukami-Kobayashi Keiko Ichikawa Yukiko Daito

- CIB Research Report 2001 -

Addresses Related to DDBJ/CIB Activities     Addresses related to the NIG mainframe computer system host name : NIG WWW server : for general inquiry on computers : for inquiry on VPP5000 (super computer) :

supernig.nig.ac.jp http://www.nig.ac.jp/ [email protected] [email protected]

Addresses of DDBJ Network Servers CIB WWW server DDBJ WWW server SAKURA WWW server anonymous-ftp server DDBJ WAIS server DDBJ gopher server

: : : : : :

http://www.cib.nig.ac.jp/ http://www.ddbj.nig.ac.jp/ http://sakura.ddbj.nig.ac.jp/ ftp.ddbj.nig.ac.jp wais.ddbj.nig.ac.jp gopher.ddbj.nig.ac.jp

: : : : : : : :

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

: : : : :

[email protected] [email protected] [email protected] [email protected] [email protected]

Addresses of DDBJ E-mail Servers FASTA E-mail server BLAST E-mail server gopher-mail get-entry E-mail server get-version E-mail server malign E-mail server SSEARCH E-mail server ssthread E-mail server

E-mail Addresses of DDBJ for for for for for

general inquiry on DDBJ data submission updating submitted data inquiry on DDBJ WWW inquiry on SAKURA

List of main databases in the NIG mainframe computer (supernig) Nucleotide Sequence Databases $DDBJ, $DDBJNEW : DDBJ periodical release and new data Amino Acid Sequence Databases $PIR : PIR periodical release $SWISS : SWISSPROT periodical release $DAD : DDBJ amino acid database Protein Three-Dimensional Structure Database $PDB : PDB periodical release この DDBJ/CIB report は無料で提供されています。 情報の引用を自由に行なうことができますが，その際ＤＤＢＪまでご一報の上，引用した旨を明記して下さい。

DDBJ/CIB Reprot March 2001 編集 / 発行 日本 DNA データバンク (DDBJ)

Edited and Published by DNA Data Bank of Japan (DDBJ)

〒 411-8540 静岡県三島市谷田 1111 国立遺伝学研究所 生命情報研究センター E-mail : [email protected] FAX : 0559-81-6849  

1111 Yata, Mishima 411-8540, Japan National Institute of Genetics, Center for Information Biology

E-mail : [email protected] FAX : +81-559-81-6849

DDBJ/CIB Report March 2001