GANESH: software for customized annotation of genome regions.
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.
Huntley
Derek
D
Department of Computing, Imperial College, London SW7 2AZ, UK.
Hummerich
Holger
H
Smedley
Damian
D
Kittivoravitkul
Sasivimol
S
McCarthy
Mark
M
Little
Peter
P
Sergot
Marek
M
D000818:Animals; D001483:Base Sequence; D002135:Calcium-Binding Proteins / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D003628:Database Management Systems; D030541:Databases, Genetic / Q000145:classification / Q000592:standards / Q000706:statistics & numerical data; D005136:Eye Proteins; D016678:Genome; D015894:Genome, Human; D018398:Homeodomain Proteins / Q000145:classification / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D020543:Proteome / Q000145:classification / Q000235:genetics; D012097:Repressor Proteins; D012984:Software; D023741:Takifugu / Q000235:genetics; D025721:WT1 Proteins / Q000145:classification / Q000235:genetics
D002135:Calcium-Binding Proteins; D005136:Eye Proteins; D018398:Homeodomain Proteins; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; C000605732:Pax6 protein, mouse; D020543:Proteome; D012097:Repressor Proteins; D025721:WT1 Proteins; C078865:reticulocalbin