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DDBJ progress report

E. Kaminuma, T. Kosuge, Y. Kodama, H. Aono, J. Mashima, T. Gojobori, H. Sugawara, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
2010 Nucleic Acids Research  
analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.  ...  In this article, we describe these new functions of the DDBJ databases and support tools.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of the DDBJ for data collection, annotation and release and for software development.  ... 
doi:10.1093/nar/gkq1041 pmid:21062814 pmcid:PMC3013661 fatcat:hqwqikzxbrhpvgsfc5fkecfzsy

DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2015 Nucleic Acids Research  
This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.  ...  The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

DDBJ progress report: a new submission system for leading to a correct annotation

Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2013 Nucleic Acids Research  
We also introduce improvements in the DDBJ services and databases made during the past year.  ...  DDBJ launched a new nucleotide sequence submission system for receiving traditional nucleotide sequence.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Keiichi Nagai and all members of DDBJ for their assistance in data collection, annotation, release and software development.  ... 
doi:10.1093/nar/gkt1066 pmid:24194602 pmcid:PMC3964987 fatcat:vc62xknuzret3iehrzgxhzqhve

DDBJ new system and service refactoring

Osamu Ogasawara, Jun Mashima, Yuichi Kodama, Eli Kaminuma, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi
2012 Nucleic Acids Research  
A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012.  ...  During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of the DDBJ for their assistance in data collection, annotation and release, and software development.  ... 
doi:10.1093/nar/gks1152 pmid:23180790 pmcid:PMC3531146 fatcat:yc6arcmponhpnkjkexwsjrul3i

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2014 Nucleic Acids Research  
The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science.  ...  We also thank Masanori Arita of the DDBJ Center for helpful discussions. We thank Mari T.  ... 
doi:10.1093/nar/gku1120 pmid:25477381 pmcid:PMC4383935 fatcat:tcpa3elm3zglbo5lauuatx3nca

DDBJ in collaboration with mass-sequencing teams on annotation

Y. Tateno
2004 Nucleic Acids Research  
The annotated data are made public at DDBJ.  ...  In the past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp) collected and released 1 066 084 entries or 718 072 425 bases including the whole chromosome 22 of chimpanzee, the wholegenome  ...  In this paper, we report our primary activity of data collection and release in the past year and our approach to the collaboration in genome annotation.  ... 
doi:10.1093/nar/gki020 pmid:15608189 pmcid:PMC539974 fatcat:jfo44562jbddrdhwtoaqdzpeh4

Complete Genome Sequence of Pseudomonas sp. Strain KUIN-1, a Model Strain for Studies on the Production of Cell-Free Ice Nucleation Proteins

Taisei Yamamoto, Yoshie Hasegawa, Hidehisa Kawahara, Hiroaki Iwaki, Frank J. Stewart
2019 Microbiology Resource Announcements  
Here, we report the 6,028,589-bp complete genome sequence of Pseudomonas sp. KUIN-1.  ...  The genome sequence reported here was deposited in DDBJ under accession number AP020337.  ...  ACKNOWLEDGMENT This work was supported by a grant-in-aid from Kansai University for progress of research in a graduate course, 2018.  ... 
doi:10.1128/mra.01204-19 pmid:31699772 pmcid:PMC6838630 fatcat:i7hmelg7pvco3nj27kgmy3lb6u

DDBJ dealing with mass data produced by the second generation sequencer

H. Sugawara, K. Ikeo, S. Fukuchi, T. Gojobori, Y. Tateno
2009 Nucleic Acids Research  
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.  ...  To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa  ...  ACKNOWLEDGEMENTS We thank all staff of DDBJ for the data collection, annotation, release, management and software development.  ... 
doi:10.1093/nar/gkn724 pmid:18927114 pmcid:PMC2686496 fatcat:ii3mg3fi5jhnnpxoym7xz76fjy

Draft Genome Sequences of Three Strains of Pseudomonas syringae pv. eriobotryae, a Pathogen Causing Canker Disease in Loquat, Isolated in Japan

Hiroaki Tashiro, Yukio Nagano, Ayaka Jiromaru, Ryunosuke Sakaguchi, Naofumi Hiehata, Shinji Fukuda, Catherine Putonti
2021 Microbiology Resource Announcements  
In this study, we report the draft genome sequences of three strains, one belonging to each of the three groups.  ...  The draft genome sequences reported here will provide fundamental information for elucidating the mechanisms of infection of P. syringae pv. eriobotryae and facilitate progress toward protection against  ...  Here, we report the draft genome sequences of three strains isolated in Japan (AM001, BM001, and CG001), one from each group.  ... 
doi:10.1128/mra.01049-20 pmid:33414289 fatcat:qlnvhik6pfesnppkuprewkejoi

DNA Data Bank of Japan dealing with large-scale data submission

H. Sugawara, S. Miyazaki, T. Gojobori, Y. Tateno
1999 Nucleic Acids Research  
DDBJ has received large scale data of Homo sapiens, Arabidopsis and Pyrococcus from Japanese researchers who made full use of the new submission system.  ...  The DNA Data Bank of Japan (DDBJ) (http//:www. ddbj.nig.ac.jp ) has developed a software system for mass submissions to cope with a recent expansion of EST and genome data submissions.  ...  In this article we report the modification of our data submission tool, Sakura (8) , and database management system, Yamato II (9) .  ... 
doi:10.1093/nar/27.1.25 pmid:9847134 pmcid:PMC148089 fatcat:zkf63jqknzgmjd6v5pzn6lyiai

Data from expressed sequence tags from the organs and embryos of parthenogenetic Haemaphysalis longicornis

Rika Umemiya-Shirafuji, Jinlin Zhou, Min Liao, Badgar Battsetseg, Damdinsuren Boldbaatar, Takeshi Hatta, Thasaneeya Kuboki, Takeshi Sakaguchi, Huey Shy Chee, Takeharu Miyoshi, Xiaohong Huang, Naotoshi Tsuji (+2 others)
2021 BMC Research Notes  
Sharing this data resource with the tick research community will be valuable for the identification of novel genes and advance the progress of tick research.  ...  The construction of each cDNA library has previously been reported [4, 5] .  ...  Although the tick species was not detected outside of quarantine until 2017, a heavy infestation of H. longicornis was recently reported in the United States [2] .  ... 
doi:10.1186/s13104-021-05740-3 pmid:34433501 pmcid:PMC8390289 fatcat:nig3of5eyjdl3iu6yvupda5a2u

Development of New DDBJ DNA Sequence Database with Data Annotation Tool Yamato II

T. Koike, T. Okayama, J. Ishii, T. Mizunuma, T. Tamura, Y. Tateno, H. Sugawara, K. Nishikawa, T. Imanishi, K. Fukami(Kobayashi), K. Ikeo, T. Gojobori
1996 Genome Informatics Series  
As the molecular biology has made a rapid progress these years, there has been a great number of changes required of the methodology for maintaining and utilizing DNA sequence data.  ...  We also take care of needs from DDBJ itself in the new system.  ...  More detailed information about this section will be reported elsewhere.  ... 
doi:10.11234/gi1990.7.157 fatcat:cxlej5bt55dvpojan4qewr2wku

Draft Genome Sequence of the Cyanotroph Pseudomonas monteilii BCN3

Lauren B. Jones, Daniel A. Kunz, David A. Baltrus
2019 Microbiology Resource Announcements  
We report here the first draft genome of Pseudomonas monteilii BCN3, a cyanotroph isolated from sewage sludge.  ...  Further identification of gene functions related to cyanotrophy are currently in progress. Data availability.  ...  The draft P. monteilii BCN3 genome sequence has been deposited in DDBJ/ENA/GenBank under the accession no. QWLL00000000. The version described here is the first version of the draft genome.  ... 
doi:10.1128/mra.01322-18 pmid:30637384 pmcid:PMC6318355 fatcat:3ubmkxzynbdjjhznmpsi22xfqi

High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

Daniel B.A. Castro, Letícia Bianca Pereira, Marcus Vinícius M. e Silva, Bárbara P. da Silva, Bruna Rafaella Z. Palermo, Camila Carlos, Daiane R.B. Belgini, Elmer Erasmo G. Limache, Gileno V. Jr Lacerda, Mariana B.P. Nery, Milene B. Gomes, Salatiel S. de Souza (+6 others)
2015 Genomics Data  
Comparative genomic analyses of SO9-6 are in progress and will be published separately.  ...  Here, we report the draft genome of K. marina SO9-6, which is the first genome from this species to be sequenced.  ... 
doi:10.1016/j.gdata.2015.05.006 pmid:26484219 pmcid:PMC4583624 fatcat:eyy74zzasnhmddpcoit6keocuu

Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype g Strain NUM4039 (JCM 30399)

Masanori Saito, Masaaki Hirasawa, Noriko Kuwahara, Tamami Okada, Koji Umezawa, Taira Kobayashi, Masaaki Okamoto, Mariko Naito, Masatomo Hirasawa, Kazuko Takada
2016 Genome Announcements  
We herein report the first complete genome sequence of A. actinomycetemcomitans serotype g strain NUM4039. The genome is 2,382,853 bp in length with a G+C content of 44.34%.  ...  tative anaerobic coccobacillus, is an important pathogen related to aggressively progressive periodontal breakdown in adolescents and adults (1) .  ...  The sequence was annotated by the DDBJ Microbial Genome Annotation Pipeline (http://migap.ddbj.nig.ac.jp).  ... 
doi:10.1128/genomea.00158-16 pmid:26988057 pmcid:PMC4796136 fatcat:n5w6ptbgorbhnpfxnaa2x4d34u
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