• (3/18~3/26) DDBJ センターの登録、検索・解析サービス停止のお知らせ
  • ホームページリニューアルと利用規約類の更新

過去のサービス

  • ホーム
  • サービス
  • 過去のサービス

Web サービス

  • GIB (2012.2. サービス終了)
  • GIB-V (2012.2. サービス終了)
  • GTPS (2012.2. サービス終了)
  • FASTA (2010.3. サービス終了)
  • PSI-BLSAT (2010.3. サービス終了)
  • SSEARCH (2010.3. サービス終了)
  • HMMPFAM (2010.3. サービス終了)
  • H-Invitational Database CIB-DDBJ Flat File Server(2009.12.31 サービス終了)
  • SRS(2008.12. サービス終了)
  • LIBRA(2008.11. サービス終了)
  • Lib score(2008.11. サービス終了)
  • SQmatch(2008.11. サービス終了)
  • PDB Retriever(2008.11. サービス終了)
  • SSThread(2007.2. サービス終了)
  • CAMUS(2007.02. サービス終了)
  • S\&W SEARCH(2006.04. サービス終了)
  • malign(2005.9. サービス終了)

E-mail サーバによる検索解析

  • get-entry
  • get-version
  • FASTA
  • BLAST
  • SSEARCH
  • S\&WSEARCH
  • ClustalW
  • HMMPFAM
  • malign

Reference

GIB

  • 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. Pubmed: 11752256

GIB-V

  • 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. Pubmed: 17158166

GTOP

  • 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. Pubmed: 12761299
  • 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. Pubmed: 12628242
  • 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. Pubmed: 12598694
  • 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. Pubmed: 12234664
  • 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. Pubmed: 11752318
  • 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. Pubmed: 11163980

GIPS

  • 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 et al
    DNA Res 2006 Dec 31;13(6):245-54. Pubmed: 17166861

HMMPFAM

  • Profile hidden Markov models.
    Eddy SR
    Bioinformatics 1998;14(9):755-63. Pubmed: 9918945
  • Pfam: a comprehensive database of protein domain families based on seed alignments.
    Sonnhammer EL, Eddy SR, Durbin R
    Proteins 1997 Jul;28(3):405-20. Pubmed: 9223186

LIBRA

  • Feasibility in the inverse protein folding protocol.
    Ota M, Nishikawa K
    Protein Sci 1999 May;8(5):1001-9. Pubmed: 10338011
  • Structural requirement of highly-conserved residues in globins.
    Ota M, Isogai Y, Nishikawa K
    FEBS Lett 1997 Sep 29;415(2):129-33. Pubmed: 9350982
  • 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. Pubmed: 9194158
  • 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. Pubmed: 7752236

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. Pubmed: 10970096

PSI-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

SSEARCH

  • Improved tools for biological sequence comparison.
    Pearson WR, Lipman DJ
    Proc Natl Acad Sci U S A 1988 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
  • Comparison of biosequences.
    Smith TF, Waterman MS.
    Adv. Appl. Math. 1981 Dec 2:482-9. Pubmed:
  • Identification of common molecular subsequences.
    Smith TF, Waterman MS
    J Mol Biol 1981 Mar 25;147(1):195-7. Pubmed: 7265238

WINA

  • 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. Pubmed: 9872398
  • 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. Pubmed: 8676743
  • 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. Pubmed: 8151715
  • 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. Pubmed: 3444411

Related pages

  • ARSA ヘルプ
  • BLAST ヘルプ
  • getentry ヘルプ
  • VecScreen ヘルプ
  • ClustalW ヘルプ
  • TXSearch ヘルプ
  • 関連論文
  • WABI (Web API for Biology)
  • WABI BLAST ヘルプ
  • WABI ClustalW ヘルプ
  • WABI VecScreen ヘルプ
  • WABI MAFFT ヘルプ
  • Pipeline ヘルプ