PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors
PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes ...
ASMC – Classifying Active Sites of Enzymes Families
ASMC method (Active Sites Modeling and Clustering) is a novel unsupervised method to classify sequences using structural information of protein pockets. The method predicts functional amino-acids by proposing active site SDP residues (Specificity Determining Position) and active site CP residues ...
GROOLS: Reactive Graph Reasoning for Genome Annotation
GROOLS (Genomic Rule Oriented Object Logic System) is a bioinformatics software that helps biologists in the evaluation of genome functional annotation through biological processes like metabolic pathways. GROOLS is an expert system that uses paraconsistent logic. It evaluates the completeness ...
NetSyn – Exploring Syntenies Networks of Genes
We developed a method to classify proteins of a family based on their conserved genomic contexts. Each protein genomic context is compared against all others to determine syntenies. A graph is generated where nodes are input proteins connected by edges ...