Download

At this time, we provide a fully functional preview of PICA models for phenotype prediction to the scientific community. Please follow these instructions:

1. Get and install the PICA software from https://github.com/univieCUBE/PICA, as described in the readme.txt.

2. Download and extract the models from http://fileshare.csb.univie.ac.at/pica/latest/models.tar.gz. New releases of the models are announced in our release newsletter. Please subscribe to stay informed. For updating models, just remove the old models folder and download and extract the new one.

3. To predict phenotypic traits for genomes and metagenomic bins, each of them needs to be transformed into a list of eggNOG 4.5 bactNOG IDs, which are present in the genome. At the moment, we recommend HMMER3 hmmscan on the bactNOG Hidden Markov Models with an e-Value threshold of 0.01. Single or multiple genotype profiles can be stored in one tab delimited text file, one genome per line, such as:

genomeid1	ENOG23444	ENOG42335	ENOG34345	................etc
genomeid2	ENOG23448	ENOG42339	ENOG34340	................etc

4. After the list of bactNOGs has been created for each genome, run predictions model by model, e.g.:

<path_to_pica>/test.py -s /path_to/your_bactNOG_genotype_profile -m /AOB/AOB.rules -t "AOB"

 

In case of problems, please do not hesitate to contact us: contact.cube@univie.ac.at. We are more than happy to help you and will continuously improve this website.