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In Silico Biology 5, 0055 (2005); ©2005, Bioinformation Systems e.V.  



u-Genome: A database on genome design in unicellular genomes

Kishore Ramaji Sakharkar1, Iti Chaturvedi2, Vincent T. K. Chow3, Chee Keong Kwoh4, Pandjassarame Kangueane2 and Meena Kishore Sakharkar2,4*

1 National University Medical Institutes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
2 Nanyang Centre for Supercomputing and Visualization, MAE, Nanyang Technological University, Singapore 639798
3 Department of Microbiology, National University of Singapore, Singapore
4 SCE, BioInformatics Research Centre, Nanyang Technological University, Singapore 639798

* Corresponding author
   N3-2C-113B, Nanyang Technological University, Singapore 639798
  Email: mmeena@ntu.edu.sg; Phone: +65-6790 5836


Edited by H. Michael; received September 16, 2005; revised and accepted November 22, 2005; published December 01, 2005


Abstract

Unicellular eukaryotes were among the first ones to be selected for complete genome sequencing because of the small size of their genomes and their interactions with humans and a broad range of animals and plants. Currently, ten completely sequenced unicellular genome sequences have been publicly released and as the number of available unicellular genomes increases, comparative genomics analysis within this group of organisms becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named u-Genome, the unicellular genome design database. The database is unique in featuring three datasets namely (1) orthologous proteins (2) paralogous proteins and (3) statistical distributions on exons, introns, intergenic DNA and correlations between them. A tool, Uniview, designed to visualize the gene structures for individual genes in the genome is also integrated. This database is of importance in understanding unicellular genome design and architecture and evolution related studies. The database is available through a web interface at http://sege.ntu.edu.sg/wester/ugenome.


Keywords: unicellular genomes, design, architecture, exon-intron lengths, paralogs, orthologs