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

Turner, Dann; Reynolds, Darren; Seto, Donald; Mahadevan, Padmanabhan

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. © 2013 Turner et al.; licensee BioMed Central Ltd.

• Journal Article Type: Article
• Publication Date: Apr 10, 2013
• Deposit Date: Sep 15, 2014
• Publicly Available Date: Nov 15, 2016
• Journal: BMC Research Notes
• Electronic ISSN: 1756-0500
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 6
• Issue: 1
• Pages: 140
• DOI: https://doi.org/10.1186/1756-0500-6-140
• Keywords: core genes, bacteriophage, taxonomy, viral genomics, data mining
• Public URL: https://uwe-repository.worktribe.com/output/933355
• Publisher URL: http://dx.doi.org/10.1186/1756-0500-6-140
• Related Public URLs: http://www.biomedcentral.com/content/pdf/1756-0500-6-140.pdf; http://creativecommons.org/licenses/by/2.0/
• Contract Date: Nov 15, 2016