2021
DOI: 10.1186/s12859-021-04501-0
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GENPPI: standalone software for creating protein interaction networks from genomes

Abstract: BackGround Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary … Show more

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Cited by 3 publications
(4 citation statements)
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“…As they mention, this type of method is not intended for the discovery of direct interactions. Recently, a new tool: GENPPI ( Anjos et al, 2021 ), allowing the generation of PPI networks by taking into account evolutionary relationships that can only be annotated from genomes, namely, conserved gene neighborhoods (CN), phylogenetic profiles (PPs), and gene fusions, has been introduced, showing that these three methods mainly allow the annotation of missing data and thus the understanding of a limited number of interactions. At present, the tool is being tested in their laboratory.…”
Section: Methods Based On Genomic Contextmentioning
confidence: 99%
See 1 more Smart Citation
“…As they mention, this type of method is not intended for the discovery of direct interactions. Recently, a new tool: GENPPI ( Anjos et al, 2021 ), allowing the generation of PPI networks by taking into account evolutionary relationships that can only be annotated from genomes, namely, conserved gene neighborhoods (CN), phylogenetic profiles (PPs), and gene fusions, has been introduced, showing that these three methods mainly allow the annotation of missing data and thus the understanding of a limited number of interactions. At present, the tool is being tested in their laboratory.…”
Section: Methods Based On Genomic Contextmentioning
confidence: 99%
“…As they mention, this type of method is not intended for the discovery of direct interactions. Recently, a new tool: GENPPI (Anjos et al, 2021), allowing the generation of PPI networks by String (Szklarczyk et al, 2019), BioGRID (Oughtred et al, 2021), Hippie (Alanis-Lobato, Andrade-Navarro and Schaefer, 2017), IntAct (Hermjakob et al, 2004a), HPRD (Keshava Keshava Prasad et al, 2009) Machine learning algorithm Supervised learning: support vector machine, artificial neural networks, naïve Bayes learning, decision trees (Sarkar and Saha, 2019;Chakraborty et al, 2021) Handling multi-dimensional and multi-variety data, high efficiency Data acquisition (massive datasets), High error susceptibility, requires significant IT resources…”
Section: Conserved Gene Neighborhoodmentioning
confidence: 99%
“…PANNOTATOR assigns color tags based on three similarity levels of alignment size and protein identity: green for certain annotations (≥95%), yellow for high similarity (<95% and ≥70%), and red for annotations with lower con dence (<70%). To assess pangenome conservation involving over two hundred genomes simultaneously, we used the GENPPI software [13]. Although initially developed for predicting protein interactions, GENPPI also generates core and accessory pangenomes for subsequent interaction analyses.…”
Section: Genomic Assembly and Bioinformatic Analysismentioning
confidence: 99%
“…Additionally, we investigated annotated proteins for conserved interactions within the genus. The GENPPI parameters were set based on examples from the software tutorial, employing dynamic neighborhood expansion and phylogenetic pro le conservations [13].…”
Section: Genomic Assembly and Bioinformatic Analysismentioning
confidence: 99%