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Open Access Technical Note

CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes

Dann Turner1, Darren Reynolds1, Donald Seto2 and Padmanabhan Mahadevan3*

Author Affiliations

1 Centre for Research in Biosciences, Faculty of Applied Sciences, University of the West of England, Bristol, BS16 1QY, UK

2 Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA

3 Department of Biology, University of Tampa, Tampa, FL, 33606, USA

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BMC Research Notes 2013, 6:140  doi:10.1186/1756-0500-6-140

Published: 8 April 2013

Abstract

Background

CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes.

Findings

CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format.

Conclusions

With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at http://binf.gmu.edu:8080/CoreGenes3.5 webcite.

Keywords:
Core genes; Bacteriophage; Taxonomy; Viral genomics; Data mining