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PuMA Release 1.2.2

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.

Authors

Josh Pace, Ken Younes-Clark, Cordell Freeman, Koenraad Van Doorslaer

University of Arizona, KVD Lab & Hurwitz Lab

Formatting Input FASTA File

>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.

PuMA Output Files

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

Dependencies

Please install the following:

• Python 3.x
• Biopython (pip)
• NCBI BLAST+ 2.7.x
• MUSCLE
• MEME, FIMO
• matplotlib (pip)
• pandas (pip)

If you do not want to install all the dependencies, consider using PuMA via Docker.

PuMA Poly Release 0.1

Polyomavirus genome annotation tool Annoates VP1, VP2, small t and Large T proteins

Authors

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

Dependencies

Please install the following:

• Python 3.x
• Biopython (pip)
• NCBI BLAST+ 2.7.x
• MUSCLE

Formatting Input FASTA File

>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)