Software & Databases

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 ...
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MICheck

MICheck (Microbial Genome checker), is a web software enabling rapid verification of sets of annotated genes and frameshifts (syntaxic annotation), in complete bacterial genomes available in public databanks. website: www.genoscope.cns.fr/agc/tools/micheck Documentation and publication: Cruveiller et al. (2005) Nucleic Acids Res ...
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AMIGene

AMIGene (Annotation of MIcrobial Genes) is an application for automatically identifying the most likely CoDing Sequences (CDSs) in a large contig or a complete bacterial genome sequence. website: www.genoscope.cns.fr/agc/tools/amigene Documentation and publication : Bocs et al. (2003)  Nucleic Acids Res. 13(31) 3723-3726 ...
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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 ...
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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 ...
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