General Technique
The GESTALT Workbench is a web-based tool for the analysis of large-scale genomic sequence data, with strong emphasis on the production of enriched graphical representation of the analyzed data. The Workbench can execute a variety of sequence analysis programs (e.g., for gene recognition and statistical sequence analyses, the resulting output files are stored in an internal database). The integrated analysis results are then visualized via sequence maps. Much biological insight can be obtained at a glance from these sequence pictorial representations, which prove to be a valuable aid in quick and intuitive sequence interpretation. The GESTALT Workbench is designed to pose minimal technical requirements on the user's end, and is locally available at http://db.systemsbiology.net/gestalt/
Purpose/use/application of the technique:
Large amounts of 'raw' genomic sequence data already exist and continue to grow exponentially. Many tools are available for automated analysis of these data by comparison to known sequences or by pattern recognition. When analyzing genomic sequences, results are often misinterpreted even though additional data are available, simply because not all the relevant knowledge is available to the researcher in an integrated and timely fashion. One of the hardest problems is how to present the sequence data and its derived annotation in an intuitive way. The GESTALT Workbench was among the first tools to enable the analysis of megabases of genomic sequence at a time. While not as comprehensive as dedicated genome browsers (e.g., the UCSC genome browser), it combines genome browsing with analytical tools and facilities for comparing sequences and building detailed gene models.
Example(s) of projects at ISB that use this technique:
The GESTALT Workbench was used at the ISB in the analysis of T-cell receptor loci; the MHC locus in human, rhesus and mouse; the Fugu runt domain genes and other Fugu genomic sequences; the loci of susceptibility to type 1 (juvenile) diabetes; and various other projects.
Ongoing area of technology development:
The GESTALT Workbench is currently the test-bed for developing new gene discovery algorithms.
Representative publication(s):
Glusman G, Lancet D. GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses. Bioinformatics. 2000 May;16(5):482-3.
Abstract
Glusman G, Lancet D. Visualizing large-scale genomic sequences. IEEE Eng Med Biol Mag. 2001 Jul-Aug;20(4):49-54.
Abstract
Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, Wang K, Koop BF, Hood L. Comparative genomics of the human and mouse T cell receptor loci.
Immunity. 2001 Sep;15(3):337-49.
Abstract
Daza-Vamenta R, Glusman G, Rowen L, Guthrie B, Geraghty DE. Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res. 2004 Aug;14(8):1501-15.
Abstract
Glusman G, Kaur A, Hood L, Rowen L. An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol. 2004 Nov 4;4(1):43.
Abstract
Smink LJ, Helton EM, Healy BC, Cavnor CC, Lam AC, Flamez D, Burren OS, Wang Y, Dolman GE, Burdick DB, Everett VH, Glusman G, Laneri D, Rowen L, Schuilenburg H, Walker NM, Mychaleckyj J, Wicker LS, Eizirik DL, Todd JA, Goodman N. T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D544-9.
Abstract
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