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Human Genome News Archive Edition

Human Genome News, March 1994; 5(6)

Data Fair Held at Genome Sequencing and Analysis Conference

The second annual Data Fair was held at the Genome Sequencing and Analysis Conference V in Hilton Head, South Carolina, on October 23-27, 1993. Scientists were offered the opportunity to use the latest sequence-analysis tools from research laboratories and commercial vendors to analyze and compare data, both published and unpublished. The fair was organized by Anthony Kerlavage [The Institute for Genomic Research (TIGR)], Jean-Michel Claverie [National Center for Biotechnology Information (NCBI)], and Fred Blattner (University of Wisconsin).

The major goal of the Data Fair was to facilitate comparison of different types of data (genomic and cDNA) from different species and provide new insights into gene expression and evolution.

All public databases available for searching were downloaded to onsite hardware including Sun and DEC workstations, Macintoshes, and a 16,000 processor MasPar. A T1 connection to the Internet allowed software to be run at remote sites. Software included Blast, FastA, Blaze, and MPSearch for sequence searching; and a variety of other clustering, filtering, and utility programs. Coding regions in ESTs were predicted using GRAIL and GENMARK and compared with translated ORFs from all genomic sequences. The recently developed MPSEARCH algorithm from John Collins (University of Edinburgh) was available on a local MasPar. In addition, on a number of electronic posters, developers of algorithms and databases demonstrated and applied the software to data brought to the fair.

Highlights of interesting results included the identification of (1) open reading frames (ORFs) in chromosome 5 of Saccharomyces cerevisiae by comparison with yeast ESTs and (2) a previously undetected gene in a human cosmid by comparison with human expressed sequence tags (ESTs), which are short known sequences on a cDNA.

Below is a summary of data brought to the meeting, including all ESTs present in dbEST. Researchers also made available some 20 million nucleotides (nt) for analysis and comparison.


For more information, contact Anthony Kerlavage at arkerlav@tigr.org.


ESTs from dbEST

  • human: 16,227
  • C. elegans: 4699
  • Arabidopsis: 2690
  • rice: 1023
  • plasmodium: 831
  • mouse: 136
  • goat: 108
  • wallaby: 36
  • maize: 16

Unpublished ESTs

  • TIGR: 16,913 (human)
  • G. Guellean: 609 (testis)
  • W. Salser: 526 (myeloid)
  • TIGR: 849 (yeast)
  • TIGR/S. Pena: 458 (schistosomiasis)
  • N. Miyadera: 3208 (rice)
  • TOTAL 48,329 (15,127,080 nt)

Genomic Sequences

  • Homo sapiens
    • E. Chen: 225 kb (Chromosomes X and Y)
    • B. Roe: 180 kb (c-abl region), 146 kb (bcr region)
    • D. Smith: 40 kb (Chromosome 10)
    • C. Martin: 47 kb (Chromosome 8)
  • S. cerevisiae
    • J. Mulligan: 420 kb (Chromosome 5)
  • M. leprae and tuberculosis
    • D. Smith: 690 kb
  • Drosophila
    • C. Martin: 77 kb
  • E. coli
    • F. Blattner: 620 kb
  • C. elegans
    • R. Wilson: 2200 kb
  • TOTAL 4,645,000 nt

HGMIS Staff

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