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Open Access Methodology article

CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes

Nikhat Zafar1, Raja Mazumder1 and Donald Seto12*

Author Affiliations

1 School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110 USA

2 Center for Biomedical Genomics and Informatics, College of Arts and Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110 USA

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BMC Bioinformatics 2002, 3:12  doi:10.1186/1471-2105-3-12

Published: 24 April 2002

Abstract

Background

Improvements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining.

Results

CoreGenes is a global JAVA-based interactive data mining tool that identifies and catalogs a "core" set of genes from two to five small whole genomes simultaneously. CoreGenes performs hierarchical and iterative BLASTP analyses using one genome as a reference and another as a query. Subsequent query genomes are compared against each newly generated "consensus." These iterations lead to a matrix comprising related genes from this set of genomes, e. g., viruses, mitochondria and chloroplasts. Currently the software is limited to small genomes on the order of 330 kilobases or less.

Conclusion

A computational tool CoreGenes has been developed to analyze small whole genomes globally. BLAST score-related and putatively essential "core" gene data are displayed as a table with links to GenBank for further data on the genes of interest. This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes webcite or http://www.bif.atcc.org/CoreGenes webcite.