Phage Annotation Tools and Methods

What is PhAnToMe

Phages, viruses that infect bacteria and archaea, 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. Despite the indisputable importance of phages in the biosphere, the annotations of phage genomes have suffered from a lack of comparative tools, which impedes the ability of researchers to interpret sequences and obtain scientifically meaningful answers. Having a consistent and accurate phage gene nomenclature is critical to phage research, and knowing which genes are viral versus bacterial or archaeal will help all researchers struggling to understand microbial genomes and metagenomes.


PhAnToMe (Phage Annotation Tools and Methods) is a platform that we are currently developing for phage genome annotations. PhAnToMe will extend the SEED database to handle the nuances of both phages and prophages, establish a consistent nomenclature for phage genes, and develop a new tool for the identification of prophages. This new resource is expected to provide high quality annotations to over 1,000 existing phage and prophage genomes and dozens of existing phage metagenomes. However, the great majority of biological researchers have little experience in computer programming. To place the tools and data available within the resource in their hands and to provide them with the ability to combine them in creative ways, biologists will be able to access PhAnToMe using BioBIKE (Biological Integrated Knowledge/programming Environment), which makes use of familiar graphical conventions to facilitate problem solving.

The workflows devised through the project will be made available to users through this interface, and likewise, workflows that users devise may be readily packaged and made available to others in the research community. A novel interactive help facility will be developed to aid new users find examples, tools, and procedures they need. PhAnToMe will enable researchers who come to the resource to answer specific questions to add their insights to the annotation as thoughts occur to them. At the same time, those who wish to bring their own sequences will be able to analyze and annotate them with the advantage of comparative analysis provided by the resource. The tools and high quality annotation developed in this project will serve as a solid basis for future efforts to comprehend phages and microbial genomes.


The text above is adapted from the PhAnToMe grant and from an abstract of PhAnToMe's first public appearance in a meeting.


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