Last updated：2016.6.7.
DDBJ Archives
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DDBJ activity
Feature Article
Column
Service in past
Terminated WWW Services
- GIB※suspended
- GIB-V※suspended
- FASTA (Service teriminated: 2010.03）
- PSI-BLSAT (Service teriminated: 2010.03）
- SSEARCH (Service teriminated: 2010.03）
- HMMPFAM (Service teriminated: 2010.03)
- H-Invitational Database CIB-DDBJ Flat File Server(Service terminated:2009.12.31）
- SRS(Service terminated:2008.12）
- LIBRA(Service terminated:2008.11）
- Lib score(Service terminated:2008.11）
- SQmatch(Service terminated:2008.11）
- PDB Retriever(Service terminated:2008.11）
- SSThread(Service terminated:2007.02）
- CAMUS(Service terminated:2007.02）
- S&W SEARCH(Service teriminated: 2006.04）
- malign(Service terminated:2005.09）
Terminated E-mail Servers
- 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.
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.
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.
- 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.
GTPS
- 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.
HMMPFAM
- 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.
LIBRA
- 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.
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.
SSEARCH
- 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.
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.
- 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
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.
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.
SSEARCH
- 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.
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.
- 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
