Marine Science Faculty Publications
Document Type
Article
Publication Date
2012
Digital Object Identifier (DOI)
https://doi.org/10.1186/1471-2105-13-37
Abstract
Background
Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose.
Results
Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http://phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study.
Conclusions
PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.
Rights Information
This work is licensed under a Creative Commons Attribution 4.0 License.
Was this content written or created while at USF?
Yes
Citation / Publisher Attribution
BMC Bioinformatics, v. 13, art. 37
Scholar Commons Citation
Dwivedi, Bhakti; Schmieder, Robert; Goldsmith, Dawn; Edwards, Robert; and Breitbart, Mya, "PhiSiGns: An Online Tool to Identify Signaturegenes in Phages and Design PCR Primers Forexamining Phage Diversity" (2012). Marine Science Faculty Publications. 738.
https://digitalcommons.usf.edu/msc_facpub/738
