These downloads are from the Phantome database. Most are generated automatically, please contact Rob Edwards or one of the other phantomers if they appear out of date and you would like more recent files.
The files are currently provided in fasta and genbank formats, and as tar and zip archives of the data. Look in the appropriate directory and the sub-directories are all organized by date. If you would like an alternative format, just let one of us know.
The DNA directory contains just the DNA sequences. In that directory there is a sub-directory called by_genome with sub-directories organized by date, that have one file per genome. There is also an all_sequences subdirectory that contains one file with the complete list of genomes, and the date included in the file name.
The proteins directory contains only the protein sequences. In that directory there is a sub-directory called by_genome with sub-directories organized by date, that have one file per genome. There is also an all_sequences subdirectory that contains one file with the complete list of genomes, and the date included in the file name.
The genomes directory contains all the genome data in a variety of formats. The genbank directory contains all genomes in genbank format, while the gff3 directory contains, you guessed it, gff3 format files
The prophages directory contains all the prophages detected by PhiSpy and phage_finder ... more details to follow.
The viruses directory currently contains all the virus sequences available in GenBank. These have not been annotated or curated.
This is a mysql dump of the database. In general this will only be useful to a few people, and I strongly encourage you to use the data in one of the other formats.
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. This work is funded by NSF grant DBI: 0850356 from the Division of Biological Infrastructure.
Please contact Rob Edwards if you would like more data, more descriptions, or more formats.