Credits and Links

We thank all who construct and maintain following databases, softwares and web sites. We are also grateful to all members in AGI sequencing teams and Arabidopsis thaliana database. This work was supported by the Kazusa DNA Research Institute Fundataion.


Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J. and Ouellette, B. F. 1998, GenBank, Nucl. Acids Res., 26, 1-7. [Medline]

GenBank overview at NCBI


Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J., 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403-410. [Medline]

Gish, W. and States, D. J., 1993, Identification of protein coding regions by database similarity search, Nature Genet., 3, 266-272. [Medline]

BLAST web site at NCBI

GENSCAN gene model (and GENSCAN suboptimal exons)

Burge, C. and Karlin, S., 1997, Prediction of complete gene structures in human genomic DNA, J. Mol. Biol., 268, 78-94. [Medline]

GENSCAN web site at MIT

Grail exons (and Grail shadow exons)

Uberbacher, E. C. and Mural, R. J., 1991, Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach, Proc. Natl. Acad. Sci. USA, 88, 11261-11265. [Medline]

Grail web site at ORNL


Brunak, S., Engelbrecht, J., and Knudsen, S. 1991, Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence, J. Mol. Biol., 220, 49-65. [Medline]

Hebsgaard, S. M., Korning, P. G., Tolstrup, N., Engelbrecht, J., Rouze, P. and Brunak, S., 1996, Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information, Nucl. Acids Res., 24, 3439-3452. [Medline]

NetGene2 web site at CBS


Kleffe, J., Hermann, K., Vahrson, W., Wittig, B. and Brendel, V., 1996, Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences, Nucl. Acids Res., 24, 4718-4728. [Medline]

Brendel, V., Kleffe, J., Carle-Urioste, J. C. and Walbot, V., 1998, Prediction of splice sites in plant pre-mRNA from sequence properties, J. Mol. Biol., 276, 85-104. [Medline]

Brendel, V. and Kleffe, J., 1998, Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA, Nucl. Acids Res., 26, 4748-4757. [Medline]

SplicePredictor web site at Stanford


Lowe, T. and Eddy, S. R., 1997, tRNAscan-SE: a Program For Improved Detection of Transfer RNA genes in Genomic Sequence, Nucl. Acids Res., 25 955-964. [Medline]

tRNAscan-SE web site at Washington Univ. in St. Louis

AGI and AtDB

AtDB's AGI general information
AtDB: Arabidopsis thaliana Database

  • The SPP Consortium (Chromosome 1)
    Stanford DNA Sequence & Technology Center, Stanford University
    The Arabidopsis thaliana Genome Center (ATGC), the University of Pennsylvania
    Plant Gene Expression Center, University of California, Berkeley
  • The TIGR Arabidopsis thaliana Database (Chromosome 2)
    The Institute for Genomic Research (TIGR)
  • KAOS: The Kazusa Arabidopsis data Opening Site (Chromosome 3 and 5)
    Kazusa DNA Research Institute
  • Arabidopsis thaliana page in GENOSCOPE (Chromosome 3)
    GENOSCOPE: Centre National de Séquençage
  • MIPS - Arabidopsis thaliana genome project (Chromosomes 4 and 5)
    John Innes Centre (JIC)
    Munich Information Centre for Protein Sequences (MIPS)
  • CSHL - Wash.U - ABI (Chromosomes 4 and 5)
    Lita Annenberg Hazen Genome Center, Cold Spring Harbor Laboratory (CSHL)
    Washington University School of Medicine Genome Sequencing Center

    Other Resources

    The Really Quite Useful MolBio Page

    Shiroinunazuna mailing list Homepage (Sorry, Japanese language only)