AtPACdb References (informal) :

Below are the reference to:
  • Arabidopsis Data

  • Methods

  • Resources

  • The Arabidopsis data:

    Chromosomal sequences:

    Five chromosomal sequences were retrieved from TAIR on 2004 April 26
    ATH1_chr1.1con.01222004 (Chromosome I)
    ATH1_chr2.1con.01222004 (Chromosome II)
    ATH1_chr3.1con.01222004 (Chromosome III)
    ATH1_chr4.1con.01222004 (Chromosome IV)
    ATH1_chr5.1con.01222004 (Chromosome V)

    EST Sequences:

    209,437 Arabidopsis EST sequences were retrieved from NCBI's dbEST database on 2004 June 29th.

    Coding Sequences(CDS):

    27,288 CDS sequences were retrived from TAIR, 2004, September 15
    ATH1_cds_cm_20040228

    Gene Names of corresponding to Tair IDs:

    Retrieved from TAIR, 2004, September 15
    TAIR_sequenced_genes

    Methods:

    BLAT--the BLAST-like alignment tool.

    Kent WJ.
    Genome Res. 2002 Apr;12(4):656-64.

    GeneSeqer@PlantGDB: Gene structure prediction in plant genomes

    Schlueter,S.D., Dong,Q. and Brendel,V.
    Nucleic Acids Res. 2003 Jul 1;31(13):3597-600

    Resources:

    Genbank.

    Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL.
    Nucleic Acids Res 2002 Jan 1;30(1):17-20

    NCBI's Stand Alone BLAST:

    Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
    Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
    "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs",
    Nucleic Acids Res. 25:3389-3402.

    NCBI dbEST.

    Boguski MS, Lowe TM, Tolstoshev CM.
    dbEST--database for "expressed sequence tags".
    Nat Genet 1993 Aug;4(4):332-3

    NCBI Taxonomy DB.

    Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
    Tatusova TA, Rapp BA (2000).
    Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res 2000 Jan 1;28(1):10-4

    GO. Gene Ontology: tool for the unification of biology.
    The Gene Ontology Consortium (2000)
    Nature Genetics 25: 25-29

    To Cite/Reference AtPACdb:

    The Arabidopsis PolyA Cleavage Site Database (AtPACdb) is currently in development and
    as such is unavailable for reference at this time. Check back in the future
    for better data, more organisms, more interface features, and hopefully a
    formal paper reference. Thanks!