A new software called GENPPI [1] is developed to create protein interaction networks from genomes.
GENPPI creates networks of interactions based on three characteristics: conserved gene neighborhoods, phylogenetic profiles, and gene fusions. This software predicts correct evolutionary relationships among species as evident from the average nucleotide identity analyses performed by the authors [1].
The working of GENPPI is based on HistoFasta Heuristic algorithm. As compared to STRING, GENPPI provides more accurate results [1]. Authors tested GENPPI on 50 genomes. It created protein interaction networks with an average size of 2200 genes in less than 40 min on a conventional computer.
GENPPI is a platform independent software written in Common Lisp without any further requirements. It is available to download at genppi.facom.ufu.br and on GitHub (https://github.com/santosardr/genppi) as well.
For more information, read here.
References
- Anjos, W.F., Lanes, G.C., Azevedo, V.A. et al. (2021). GENPPI: standalone software for creating protein interaction networks from genomes. BMC Bioinformatics 22, 596.
