GIS: a web-based genomics information system for efficiently manipulating and accessing genome physical maps
Abstract
Biological science has entered the genome era. Global genome integrative physical and genetic mapping promises to revolutionize modern genomics research. To facilitate manipulation and applications of the results from genomics research, many databases, web sites and information pools have been developed. However, these databases deal with DNA or protein data, such as genes, ESTs (expressed sequence tags), DNA markers, DNA sequences, and genetic maps. Few databases comprehensively deal with genome-wide integrated physical and genetic maps. In this study, we have created a database and developed a web-based genomics information system (GIS) especially dealing with the data resulting from physical mapping of agricultural genomes by fingerprint analysis of large-insert BAC (bacterial artificial chromosomes) and BIBACs (binary BACs), and integration with genetic maps using DNA markers and ESTs. This database includes clones, bands, fingerprints, gels, contigs, DNA markers, ESTs, genes, DNA marker and EST positive clones, and integrated physical and genetic graphic maps. The GIS consists of three main domains: web-based User Interface (UI), Common Gateway Interface (CGI) and Database (DB). It allows users directly to access the database via World Wide Web (http://hbz.tamu.edu), to capture, view, compare and analyze their results against our database, and to identify and select BAC and BIBAC clones and/or contigs containing their DNA markers and/or overlapping with their clones from our physical maps based on the BAC fingerprint similarity. The database and GIS were extensively tested using the rice and Arabidopsis physical mapping data and results generated in our laboratory. The testing results indicate that the GIS is easy to access via WWW, friendly user-interfaced, fully-functioned, and fault-tolerant. It is applicable to manipulation of physical mapping database of different plant and animal species. A web page for use of the system has been posted at http://hbz.tamu.edu/GIS.
Description
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Includes bibliographical references (leaves 24-25).
Issued also on microfiche from Lange Micrographics.
Includes bibliographical references (leaves 24-25).
Issued also on microfiche from Lange Micrographics.
Keywords
plant physiology., Major plant physiology.