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DDBJ progress report
2010
Nucleic Acids Research
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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
2015
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
2012
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2004
Nucleic Acids Research
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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
2019
Microbiology Resource Announcements
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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
2009
Nucleic Acids Research
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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
2021
Microbiology Resource Announcements
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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
1999
Nucleic Acids Research
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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
2021
BMC Research Notes
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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
1996
Genome Informatics Series
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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
2019
Microbiology Resource Announcements
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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
2015
Genomics Data
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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)
2016
Genome Announcements
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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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