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GENPPI- Tool to create protein interaction networks from genomes.

Tariq Abdullah

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genppi

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

  1. 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.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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