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Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.
Fumoto M, Miyazaki S, Sugawara H.
Nucleic Acids Res. 2002 Jan 1;30(1):66-8.


Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.
Hirahata M, Abe T, Tanaka N, Kuwana Y, Shigemoto Y, Miyazaki S, Suzuki Y, Sugawara H.
Nucleic Acids Res. 2007 Jan;35(Database issue):D339-42.


Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.
Nakashima H, Fukuchi S, Nishikawa K.
J Biochem. 2003 Apr;133(4):507-13.
Unique amino acid composition of proteins in halophilic bacteria.
Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K.
J Mol Biol. 2003 Mar 21;327(2):347-57.
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.
Fukami-Kobayashi K, Tateno Y, Nishikawa K.
Mol Biol Evol. 2003 Feb;20(2):267-77.
A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K.
Gene. 2002 Jul 10;294(1-2):25-33.
GTOP: a database of protein structures predicted from genome sequences.
Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K.
Nucleic Acids Res. 2002 Jan 1;30(1):294-8.
Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.
Kawabata T, Arisaka F, Nishikawa K.
Gene. 2000 Dec 23;259(1-2):223-33.


Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).
Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H.
DNA Res. 2006 Dec 31;13(6):245-54. Epub 2006 Dec 13.


Profile hidden Markov models.
Eddy SR.
Bioinformatics. 1998;14(9):755-63.
Pfam: a comprehensive database of protein domain families based on seed alignments.
Sonnhammer EL1, Eddy SR, Durbin R.
Proteins. 1997 Jul;28(3):405-20.


Feasibility in the inverse protein folding protocol.
Ota M, Nishikawa K.
Protein Sci. 1999 May;8(5):1001-9.
Structural requirement of highly-conserved residues in globins.
Ota M, Isogai Y, Nishikawa K.
FEBS Lett. 1997 Sep 29;415(2):129-33.
Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins.
Ota M, Nishikawa K.
Protein Eng. 1997 Apr;10(4):339-51.
Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H.
Ota M, Kanaya S, Nishikawa K.
J Mol Biol. 1995 May 12;248(4):733-8.

Lib score

An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries.
Udaka K, Wiesmüller KH, Kienle S, Jung G, Tamamura H, Yamagishi H, Okumura K, Walden P, Suto T, Kawasaki T.
Immunogenetics. 2000 Aug;51(10):816-28.


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.


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.
Comparison of biosequences.
Smith TF, Waterman MS.
Adv. Appl. Math. 1981 Dec 2:482-9. doi:10.1016/0196-8858(81)90046-4
Identification of common molecular subsequences.
Smith TF, Waterman MS.
J Mol Biol. 1981 Mar 25;147(1):195-7.


Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase.
Ishimizu T, Endo T, Yamaguchi-Kabata Y, Nakamura KT, Sakiyama F, Norioka S.
FEBS Lett. 1998 Dec 4;440(3):337-42.
Large-scale search for genes on which positive selection may operate.
Endo T, Ikeo K, Gojobori T.
Mol Biol Evol. 1996 May;13(5):685-90.
Reduction of synonymous substitutions in the core protein gene of hepatitis C virus.
Ina Y, Mizokami M, Ohba K, Gojobori T.
J Mol Evol. 1994 Jan;38(1):50-6.
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei M, Gojobori T.
Mol Biol Evol. 1986 Sep;3(5):418-26