PhAnToMe

Tools

What can you do with PhAnToMe?

• Access and browse phage genomes and all proteins encoded therein: Phage SEED
• Access phage genomes and proteins, perform different levels of sequence and genome analysis: Phage BioBike
• View and download the metadata for phage genomes and submit metadata information: Phage Metadata or forms within SEED
• See the distribution of phages in different ecosystems: Phage Eco-Locator
• See the current version of the Phage Proteomic Tree
• Use the "Classic" Repeat Finder to determine phage starts and ends for phage genomes integrated in microbial genomes, or more generally to detect repeats in phage genomes
• Use PhiHunter

Soon you will be able to:

• Upload a fasta-formatted or Genbank-formatted phage sequence and have it annotated in about 24 hours or less (Phage RAST Beta—in final preparation). Update: The test version of phiRAST has been running since Sep 1 2010 and has been already updated twice since. This version will be made public very soon, but we want to make sure it has been tested enough before its release. If you wish to have your newly sequenced phage genomes annotated and would like to be one of the phiRAST testers, please This email address is being protected from spambots. You need JavaScript enabled to view it. .
• Design and execute your own BioBike programs to access, analyze, and compare phage genomes and phage proteins.
• Upload your metagenomes to Eco-Locator and determine the distribution of the metagenomic sequences in all phage genomes in the PhAnToMe database

If you use this work, please cite the following sources:

For subsystems and phage SEED, the current references are:

• "The SEED: a peer-to-peer environment for genome annotation." Communications of the ACM archive Volume 47 , Issue 11 (November 2004)
• "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes." Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. PMID: 16214803
• "Accessing the SEED genome databases via Web services API: tools for programmers." BMC Bioinformatics. 2010 Jun 14;11:319. PMID: 20546611

For RAST, the Rapid Annotation pipeline, use:

• "The RAST Server: rapid annotations using subsystems technology." BMC Genomics. 2008 Feb 8;9:75. PMID: 18261238

For BioBike, use:

• "BioBIKE: a Web-based, programmable, integrated biological knowledge base." Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W28-32. Epub 2009 May 11. PMID: 19433511

If you use unpublished work, please contact us!