PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.
Phages (viruses that infect bacteria) are the most abundant biological entities on the planet. Phages have been central to many molecular biology tools and discoveries, and serve important ecological functions, including structuring microbial communities, driving evolution through horizontal gene transfer, and playing major roles in biogeochemical cycling. Unlike cellular organisms, there is no single gene that is found in all phages. This presents a real challenge for their identification and characterization, especially in environmental samples. Closely-related phages do contain homologous conserved genes (or signature genes) that can be used to define evolutionary relationships amongst them. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers that can be used to amplify related genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose. Here we present PhiSiGns, a bioinformatics tool that allows biologists to perform a dynamic search against selected phage genomes of interest, identify signature genes, generate sequence alignments, and design primers for PCR amplification, all in one environment.
PhiSiGns is a product of the Breitbart lab (http://www.marine.usf.edu/genomics). This work is funded by the National Science Foundation (NSF) grant (DBI-0850206 and DBI-0850356) from the Division of Biological Infrastructure as part of the PhAnToMe project (http://www.phantome.org). PhiSiGns is available at http://www.phantome.org/phisigns/
If you use this tool, please cite as: Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, and Mya Breitbart (in review): PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.