Services in past

Terminated WWW Services

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

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

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

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

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

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

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

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

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

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

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