Name: PPANINI
User manual || Tutorial
Description: PPANINI (Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration) provides a computational pipeline to prioritize microbial genes based on their metagenomic properties (e.g. prevalence and abundance). The resulting prioritized list of gene candidates can then be analyzed further using our visualization tools.
PPANINI prioritizes important genes in a microbial community based on presence/absence and abundance from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. PPANINI takes a genes abundances table for all the samples in a study, it ranks the important genes and summarize the outputs as:
- A table of prioritized important genes with prevalence, abundance, and a score (PPANINI score). The genes are ranked based on their PPANINI score. In the genes column PPANINI uses UniRef90 ids or inartificial centroid for similar genes.
A final abundances table can be used to start if it exists, or PPANINI can generate it from short reads.
Citation
Gholamali Rahnavard, Afrah Shafquat, Himel Mallick, Jason Lloyd-Price, Kevin Bonham, Bahar Sayoldin, Eric A. Franzosa, Curtis Huttenhower, Identifying important uncharacterized genes using metagenomes and metatranscriptomes . huttenhower.sph.harvard.edu/ppanini