Last updated:2016.4.15.

How to Use DDBJ

Please acknowledge

The activity of the DDBJ and NIG Supercomputer System are evaluated by the acknowledgments of all of you.
Please acknowledge in your papers, presentations and other publications, the role of DDBJ services and/or NIG Supercomputer System played in your research.

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 <DDBJ>
 This research was performed using "name of DDBJ Service, analytical tools".
 < NIG Supercomputer System>
 Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.
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Reference
The latest paper about the DDBJ
Reference
How to Create Links to DDBJ Entries

Basic Knowledge

Contents

DDBJ HP

FAQ / DRA FAQ
Web Service Help
The help page are linked by each service
WABI help
WABI is a web API for using the search services of the DNA Data Bank of Japan (DDBJ) without needing to navigate the web front-end.
DDBJ Movies
Contact us

References

DDBJ

DNA data bank of Japan (DDBJ) progress report.
Mashima J, Kodama Y, Kosuge T, Fujisawa T, Katayama T, Nagasaki H, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T.
Nucleic Acids Res. 2016 Jan 4;44(D1):D51-7. doi: 10.1093/nar/gkv1105

ARSA ・ TXSearch

DDBJ new system and service refactoring.
Ogasawara O, Mashima J, Kodama Y, Kaminuma E, Nakamura Y, Okubo K, Takagi T.
Nucleic Acids Res. 2013 Jan;41(Database issue):D25-9. doi: 10.1093/nar/gks1152

BLAST

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.
PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation.
Zhang J, Madden TL.
Genome Res. 1997 Jun;7(6):649-56.
Applications of network BLAST server.
Madden TL, Tatusov RL, Zhang J.
Methods Enzymol. 1996;266:131-41.
Identification of protein coding regions by database similarity search.
Gish W, States DJ.
Nat Genet. 1993 Mar;3(3):266-72.
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.
J Mol Biol. 1990 Oct 5;215(3):403-10.
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
Karlin S, Altschul SF.
Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264-8.

ClustalW

Multiple sequence alignment with the Clustal series of programs.
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD.
Nucleic Acids Res. 2003 Jul 1;31(13):3497-500.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ.
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80.

DDBJ Read Annotation Pipeline

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.
Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y.
DNA Res. 2013 Aug;20(4):383-90. doi: 10.1093/dnares/dst017
DDBJ launches a new archive database with analytical tools for next-generation sequence data.
Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y.
Nucleic Acids Res. 2010 Jan;38(Database issue):D33-8. doi: 10.1093/nar/gkp847

DDBJ Sequence Read Archive

The Sequence Read Archive: explosive growth of sequencing data.
Kodama Y, Shumway M, Leinonen R; International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res. 2012 Jan;40(Database issue):D54-6. doi: 10.1093/nar/gkr854.
The sequence read archive.
Leinonen R, Sugawara H, Shumway M; International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21. doi: 10.1093/nar/gkq1019.

FASTA

Improved tools for biological sequence comparison.
Pearson WR, Lipman DJ.
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8.
Rapid and sensitive protein similarity searches.
Lipman DJ, Pearson WR.
Science. 1985 Mar 22;227(4693):1435-41.
Rapid similarity searches of nucleic acid and protein data banks.
Wilbur WJ, Lipman DJ.
Proc Natl Acad Sci U S A. 1983 Feb;80(3):726-30.

Japanese Genotype-phenotype Archive (JGA)

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data.
Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y.
Nucleic Acids Res. 2015 Jan;43(Database issue):D18-22. doi: 10.1093/nar/gku1120. 2015 Jan

MUFFT

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Katoh K, Standley DM.
Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010.
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
Kuraku S, Zmasek CM, Nishimura O, Katoh K.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. doi: 10.1093/nar/gkt389.
Adding unaligned sequences into an existing alignment using MAFFT and LAST.
Katoh K, Frith MC.
Bioinformatics. 2012 Dec 1;28(23):3144-6. doi: 10.1093/bioinformatics/bts578.
Parallelization of the MAFFT multiple sequence alignment program.
Katoh K, Toh H.
Bioinformatics. 2010 Aug 1;26(15):1899-900. doi: 10.1093/bioinformatics/btq224.
Multiple alignment of DNA sequences with MAFFT.
Katoh K, Asimenos G, Toh H.
Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
Katoh K, Toh H.
BMC Bioinformatics. 2008 Apr 25;9:212. doi: 10.1186/1471-2105-9-212.
Recent developments in the MAFFT multiple sequence alignment program.
Katoh K, Toh H.
Brief Bioinform. 2008 Jul;9(4):286-98. doi: 10.1093/bib/bbn013.
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
Katoh K, Toh H.
Bioinformatics. 2007 Feb 1;23(3):372-4.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
Katoh K, Kuma K, Toh H, Miyata T.
Nucleic Acids Res. 2005 Jan 20;33(2):511-8.
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T.
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66.

MiGAP

Microbial Genome Annotation Pipeline (MiGAP) for diverse users
Sugawara H, Ohyama A, Mori H and Kurokawa K. (2009)
The 20th International Conference on Genome Informatics (GIW2009) Poster and Software Demonstrations (Yokohama) S001-1-2
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
Noguchi H, Taniguchi T, Itoh T.
DNA Res. 2008 Dec;15(6):387-96. doi: 10.1093/dnares/dsn027
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW.
Nucleic Acids Res. 2007;35(9):3100-8.
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.
BMC Bioinformatics. 2003 Sep 11;4:41.
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL.
Nucleic Acids Res. 1999 Dec 1;27(23):4636-41.
A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ.
Science. 1997 Oct 24;278(5338):631-7.
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Lowe TM, Eddy SR.
Nucleic Acids Res. 1997 Mar 1;25(5):955-64.
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.
J Mol Biol. 1990 Oct 5;215(3):403-10.
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