Nucleic Acids Research, 2005, Vol. 33, Database issue D303-D307
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
PartiGeneDB—collating partial genomes
1 Program in Genetics and Genomic Biology and 2 Program in Structural Biology and Biochemistry, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, 3 Department of Biochemistry and 4 Department of Medical Genetics and Molecular Biology, University of Toronto, Toronto, Ontario, Canada M5S 1A1
* To whom correspondence should be addressed. Tel: +1 416 813 5746; Fax: +1 416 813 5022; Email: jparkin{at}sickkids.ca
Received August 13, 2004; Revised and Accepted October 18, 2004
Owing to the high costs involved, only 28 eukaryotic genomes have been fully sequenced to date. On the other hand, an increasing number of projects have been initiated to generate survey sequence data for a large number of other eukaryotic organisms. For the most part, these data are poorly organized and difficult to analyse. Here, we present PartiGeneDB (http://www.partigenedb.org), a publicly available database resource, which collates and processes these sequence datasets on a species-specific basis to form non-redundant sets of gene objects—which we term partial genomes. Users may query the database to identify particular genes of interest either on the basis of sequence similarity or via the use of simple text searches for specific patterns of BLAST annotation. Alternatively, users can examine entire partial genome datasets on the basis of relative expression of gene objects or by the use of an interactive Java-based tool (SimiTri), which displays sequence similarity relationships for a large number of sequence objects in a single graphic. PartiGeneDB facilitates regular incremental updates of new sequence datasets associated with both new and exisitng species. PartiGeneDB currently contains the assembled partial genomes derived from 1.83 million sequences associated with 247 different eukaryotes.
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