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Genome Res. 13:2195-2202, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/03 $5.00
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GANESH: Software for Customized Annotation of Genome Regions

Derek Huntley1, Holger Hummerich2, Damian Smedley3, Sasivimol Kittivoravitkul1, Mark McCarthy3, Peter Little4 and Marek Sergot1,5

1 Department of Computing, Imperial College, London SW7 2AZ, UK 2 Medical Research Council Prion Unit/Department of Neurodegenerative Diseases, Institute of Neurology, London WC1N 3BG, UK 3 School of Medicine, Imperial College, London W6 8RP, UK 4 School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney 2052, Australia

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.698103.

5 Corresponding author.
E-MAIL mjs{at}doc.ic.ac.uk; FAX 44-20-7581-8024.


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Copyright © 2003 by Cold Spring Harbor Laboratory Press.