title: PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery.
abstract: As the exponential growth of DNA sequence information in databases continues, the task of converting this deposited information into knowledge becomes more dependent on integrative sequence analysis and visualization tools. PANORAMA is an Internet-accessible software package that performs a variety of informatics analyses on a given DNA sequence and returns a visual and interactive representation of the results. Its design is modular, so that further sequence analysis tools can be integrated with minimal effort. The utility of PANORAMA is demonstrated in the analysis of 650 kb of human genomic DNA from chromosome region 3p21.3, a region of potential tumor suppressor genes involved in lung cancer, breast cancer, and other forms of cancer. PANORAMA aided in the discovery of genes and alternate splice forms of known exons, in the demarcation of intron-exon boundaries, and in the identification of promoter regions and polymorphisms, all of which contributed to a better understanding of the region. PANORAMA is available on the World Wide Web at http://atlas.swmed.edu.
authors.affiliation: Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
authors.forename: A
authors.initials: A
authors.lastname: Pertsemlidis
authors.forename: A
authors.initials: A
authors.lastname: Pande
authors.forename: B
authors.initials: B
authors.lastname: Miller
authors.forename: P
authors.initials: P
authors.lastname: Schilling
authors.forename: M H
authors.initials: MH
authors.lastname: Wei
authors.forename: M I
authors.initials: MI
authors.lastname: Lerman
authors.forename: J D
authors.initials: JD
authors.lastname: Minna
authors.forename: H R
authors.initials: HR
authors.lastname: Garner
authors.forename: D
authors.initials: D
authors.lastname: Mittelman
mesh_terms: D000818:Animals; D018899:CpG Islands; D004247:DNA / Q000235:genetics; D020224:Expressed Sequence Tags; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA