References

Latest publication regarding DDBJ Center

• DDBJ update: streamlining submission and access of human data.
  Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O
  Nucleic Acids Res 2021 Jan 8;49(D1):D71-D75. Pubmed: 33156332

ARSA

• 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. Pubmed: 23180790

TXSearch

• DNA Data Bank of Japan.
  Mashima J, Kodama Y, Fujisawa T, Katayama T, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T
  Nucleic Acids Res2017 Jan 4;45(D1):D25-D31. Pubmed: 27924010

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. Pubmed: 9254694
• 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. Pubmed: 9199938
• Applications of network BLAST server.
  Madden TL, Tatusov RL, Zhang J
  Methods Enzymol 1996;266():131-41. Pubmed: 8743682
• Identification of protein coding regions by　database similarity search.
  Gish W, States DJ
  Nat Genet 1993 Mar;3(3):266-72. Pubmed: 8485583
• Basic local alignment search tool.
  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ
  J Mol Biol1990 Oct 5;215(3):403-10. Pubmed: 2231712
• 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 A1990 Mar;87(6):2264-8. Pubmed: 2315319

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. Pubmed: 12824352
• 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 Res1994 Nov 11;22(22):4673-80. Pubmed: 7984417

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 et al
  DNA Res 2013 Aug;20(4):383-90. Pubmed: 23657089
• 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 Res2010 Jan;38(Database issue):D33-8.Pubmed: 19850725

DDBJ Sequence Read Archive

• The Sequence Read Archive: explosive growth of sequencing data.
  Kodama Y, Shumway M, Leinonen R
  Nucleic Acids Res2012 Jan;40(Database issue):D54-6.Pubmed: 22009675

Genomic Expression Archive (GEA)

• DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.
  Kodama Y, Mashima J, Kosuge T, Ogasawara O
  Nucleic Acids Res24 October 2018 Pubmed: 30357349

Japanese Genotype-phenotype Archive (JGA)

• DDBJ update: streamlining submission and access of human data.
  Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O
  Nucleic Acids Res 2021 Jan 8;49(D1):D71-D75. Pubmed: 33156332

MAFFT

• 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. Pubmed: 23329690
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
  Katoh K, Misawa K, Kuma K, Miyata T
  Nucleic Acids Res2002 Jul 15;30(14):3059-66. Pubmed: 12136088

FASTA

This service is provided in the NIG Supercomputer only.

• Improved tools for biological sequence comparison.
  Pearson WR, Lipman DJ
  Proc Natl Acad Sci U S A1988 Apr;85(8):2444-8. Pubmed: 3162770
• Rapid and sensitive protein similarity searches.
  Lipman DJ, Pearson WR
  Science 1985 Mar 22;227(4693):1435-41. Pubmed: 2983426

• Rapid similarity searches of nucleic acid and protein data banks.
  Wilbur WJ, Lipman DJ
  Proc Natl Acad Sci U S A1983 Feb;80(3):726-30. Pubmed: 6572363

• DDBJ activity papers (2009-)
• Papers of the service that DDBJ provided in the past.