This folder contains the data and the script to generate PANTHER Generic Mapping files for 1169 genomes from the Reference Proteome Project that are not one of the 143 genomes in the PANTHER database. 

A complete list of the genomes, and number of IDs that can be mapped to PANTHER, can be found in the 'stats' file. Check to see if the organism you are interested in is in it before proceed. The genome name used here is a combination of the species name (plus strain name if more than one strain is available for a particular speccies) and the organism mnemonic (a 5-letter symbol) to specify the strain. For details of the organism mnemonic, please visit: https://www.uniprot.org/taxonomy/

The 'stats' file contains 3 columns. The first column is the genome name described above. The second column is the total number of genes in the genome. The third column is the number genes that have a PANTHER annotation.

Here are some examples of the genome names used here:
Aspergillus_carbonarius_ASPC5
Aspergillus_clavatus_ASPCL
Aspergillus_flavus_ASPFA
Aspergillus_flavus_ASPFN
Vibrio_sp_VIBSJ
Vibrio_sp_VIBSN
Xenopus_laevis_XENLA

BASCIS INFORMATION

PANTHER Version: v.18.0
Reference Proteome Version: 2023-03

Procedures:

1. Uncompress the classification file by running the following commands
> gunzip panther_classification.tar.gz
> tar -xvf panther_classification.tar
2. Prepare your input gene list file. It should be a tab-deliminated simple text file, with the ID in the first column. Currently only the UniProtKB IDs are supported for this process.
3. Here is how it can be run.
> cd map_genomes_to_PANTHER/
> perl map_panther.pl -i panther_classification/[the genome classification] -g [your gene list] > output
4. The output file can be used directly as an input to the PANTHER gene list analysis tool. Make sure to select the "PANTHER Generic Mapping File" as the List Type.

There is a test gene list in the folder. You can run the following command to test:

perl map_panther.pl -i panther_classification/Endocarpon_pusillum_ENDPU -g test_geneList > test.out