PhAnToMe

Art...		science...		and fun

Phages (viruses that infect bacteria) are the most abundant biological entities on the planet and are powerful cogs in the Earth System. However, the annotation of phage genomes and metagenomes lags behind their microbial counterparts due to historical bottlenecks.

The PhAnToMe—PHage ANnotation TOols and MEthods—project was launched with NSF funding to establish a phage annotation database, a visual programming interface (Phage BioBike), and a rapid annotation pipeline for phage genomes (PhiRAST—phage Rapid Annotation Using Subsystem Technology).

The Phantome project consists of many components: our PhageSeed database is an integration of all sequenced phage genomes, and also provides access to prophages, bacterial genomes, and more. The PhiRAST software that we are developing with colleagues at Argonne National Labs and the Fellowship for Interpretation of Genomes allows rapid annotation of phage genomes from a fasta DNA sequence file. PhageBioBike provides a graphical programming language for accessing data in the PhageSeed database, providing a more robust way to access the data.

Why use PhAnToMe project tools?

1. Updated phage database: We provide the curation needed to accurately annotate viral genomes and metagenomes. Specifically, we have…
   • Developed viral subsystems to establish systematic ontology^**
   • Identified prophages in microbial genomes
   • Incorporated mobile element information from ACLAME and other databases
   • Keep our databases updated and comprehensive for relevant "phage" information


2. Novel tools and methods: We provide new algorithms and visualization tools that we or others develop as needed for comparative genomics and metagenomics. If you'd like something here, This e-mail address is being protected from spambots. You need JavaScript enabled to view it .
   • Genomics: Comparative genomics synteny mapper, repeat finder, phage proteomic tree, EcoLocator
   • Metagenomics: Coming soon!
   • Phage diversity tools: phageSIGNS


3. Custom informatics pipelines: phage BioBIKE allows users to modularly (using existing public use 'components') or de novo establish their own informatic pipelines, and 'publish' those to public use space.

Click Tools on the top menu to see what's available and get started.

PhAnToMe status, as of September 2010:

660 phage genomes, 7689 phage proteins classified into subsystems, 591 phage genomes compared against 296 metagenomes.

^**Please note that PhAnToMe is a constantly improving product that benefits from continued expert curation of viral subsystems (we are not experts on all things viral). If you would like to become an expert reviewer, please This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

PhAnToMe is a NSF-funded collaborative project of research centers at San Diego State University, University of South Florida, University of Arizona, and University of Virginia. (See PhAnToMers in the top menu for more information.)