Welcome to PhAnToMe!
PhAnToMe Status - 2013
The PhAnToMe project is no longer funded and so the pace of work has slowed considerably. We still maintain the Phage SEED and biobike servers, available from the Tools menu. The Phage SEED now has over 1,000 complete phage genomes, and our comparative tools (such as the phage proteomic tree) continue to be updated.
All PhAnToMe subsystems are in the Public SEED and we continue to add new annotations and updates.
Downloads of all our data remain available and are updated automatically on the first of the month.
Welcome to PhAnToMe!
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?
- 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
- Genomics: Comparative genomics synteny mapper, repeat finder, phage proteomic tree, EcoLocator
- Metagenomics: Coming soon!
- Phage diversity tools: phageSIGNS
- 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 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.)