(click to be directed to the Read the Docs documentation (more detailed))
Papillomavirus genome annotation tool.
PuMA through iMicrobe is currently down. We will try to restore functionality ASAP
PuMA is now available to access through Docker.
Release 1.2.2 (1/30/2023) fixed a strange bug in the linearization process Release 1.2.1 (7/28/2020) added gene alignment verification, ability to handle a multi genome input fasta file, and updated databases.
Josh Pace, Ken Younes-Clark, Cordell Freeman, Koenraad Van Doorslaer
University of Arizona, KVD Lab & Hurwitz Lab
>Short name|Full Name
Sequence
Short name is the abbreviation or accession number you want for output files (e.g. HPV16)
Full name is what will be printed to the screen (e.g. Human papillomavirus 16)
For a multi genome file, follow the same naming convention as above.
Within the puma_out folder, there is a log file that has information from execution and there will be a folder for each genome named with the "Short name". Within each "Short name" folder there are 'for_user' and 'program_files' folders. Within the for_user folder there are:
- csv file containing start, stop, nucleotide and protein sequences
- a graphical output of the open reading frames and miscellaneous features
- genbank file
- gff3 file
- .fsa file
- .tbl file
Please install the following:
If you do not want to install all the dependencies, consider using PuMA via Docker.
Polyomavirus genome annotation tool Annoates VP1, VP2, small t and Large T proteins
Josh Pace, Ken Younes-Clark, Koenraad Van Doorslaer
University of Arizona, KVD Lab & Hurwitz Lab
Release 0.1 (7/25/19) output is printed genome information and csv
Please install the following:
>Short name|Full Name
Sequence
Short name is the abbreviation or accession number you want for output files (e.g. SV40a)
Full name is what will be printed to the screen (e.g. simian virus 40)