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