Abstract
BackgroundCoreGenes3.5 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.FindingsCoreGenes3.5 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.ConclusionsWith 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.
Highlights
CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process
Genes that are common between a set of genomes are known as core genes
The input to CoreGenes3.5 consists of a reference genome and a query genome
Summary
The batch processing feature of CoreGenes3.5 enables researchers to analyze multiple small genomes expeditiously using a web interface. This allows users to data mine the increasing numbers of genomes in sequence databases and to determine quickly the phylogenetic relationships amongst them. Availability and requirements Project name: CoreGenes3.5 Project home page: http://binf.gmu.edu:8080/Core Genes3.5 Operating system(s): Platform independent Programming language: Java Any restrictions to use by non-academics: License required for commercial usage. Competing interests The authors declare that they have no competing interests. Authors’ contributions DT and PM implemented the batch processing in CoreGenes3.5. DT, DR, DS, and PM wrote the manuscript. All authors read and approved the final manuscript
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