Search and Analysis service References

Overall References for DDBJ Services

DDBJ HP

Help Pages for Current Web Services

getentry | ARSA | BLAST | ClustalW | TXSearch | VecScreen |GTOP | PMD


Original Articles and Related Articles

FASTA | BLAST | PSI-BLAST | SSEARCH | HMMPFAM | ClustalW | GIB | GIB-V | GTPS | GTOP | PMD | WINA

FASTA

Original Articles
  • Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
  • Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity searches. Science. 227(4693):1435-41.
Related Articles
  • Wilbur WJ, Lipman DJ. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 80(3):726-30.

BLAST

Original Articles
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402.
Related Articles
  • Zhang J, Madden TL. (1997) PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and notation. Genome Res.7(6):649-56.
  • Madden TL, Tatusov RL, Zhang J. (1996) Applications of network BLAST server. Methods Enzymol. 266:131-41.
  • Gish W, States DJ. (1993) Identification of protein coding regions by database similarity search. Nat Genet. 3(3):266-72.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
  • Karlin S, Altschul SF. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A. 87(6):2264-8.

PSI-BLAST

Original Articles
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402.

SSEARCH

Original Articles
  • Smith TF, Waterman MS. (1981) Comparison of biosequences. Adv. Appl. Math. 2:482-9.
  • Smith TF, Waterman MS. (1981) Identification of common molecular subsequences. J Mol Biol. 147(1):195-7.
Related Articles
  • Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
  • Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity searches. Science. 227(4693):1435-41.

HMMPFAM

Original Articles
  • Sonnhammer EL, Eddy SR, Durbin R. (1997) Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments. Proteins, 28:405-420
  • Eddy SR. (1998) Profile Hidden Markov Models. Bioinformatics, 14:755-763

ClustalW

Original Articles
  • Thompson JD, Higgins DG, Gibson TJ. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80.
Related Articles
  • Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31(13):3497-500.

GIB

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

GIB-V

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

GTPS

Original Articles
  • 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, and Sugawara H. (2006) 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). DNA Res. 2006 Dec 31;13(6):245-54.

GTOP

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

PMD

Original Articles
  • Kawabata T, Ota M, Nishikawa K. (1999) The Protein Mutant Database. Nucleic Acids Res. 27(1):355-7.
Related Articles
  • Nishikawa K, Ishino S, Takenaka H, Norioka N, Hirai T, Yao T, Seto Y. (1994) Constructing a protein mutant database. Protein Eng. 7(5):73

LIBRA

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

Lib score

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

WINA

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


Archives

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
  • ClustalW
  • HMMPFAM
  • S&W SEARCH
  • m-align
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