Abstract Background In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss informationwhen parts alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. Results paper, HIV (Human Immunodeficiency Virus) SIV (Simian data used evaluate method. The...

Norine is the first database entirely dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. It performed by huge protein complexes synthetases (NRPSs). The molecules synthesized NRPS contain a high proportion of nonproteogenic amino acids. primary structure these not always linear but often more complex may cycles branchings. recent...

Nonribosomal peptides (NRPs) are molecules produced by microorganisms that have a broad spectrum of biological activities and pharmaceutical applications (e.g., antibiotic, immunomodulating, antitumor activities). One particularity the NRPs is biodiversity their monomers, extending far beyond 20 proteogenic amino acid residues. Norine, comprehensive database NRPs, allowed us to review for first time main characteristics especially monomer biodiversity. Our analysis highlighted significant...

Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well that promote plant growth. We have carried out global strategy, which combined two complementary approaches. The first one genome guided with deep analysis sequences and the second assay experiments to support predictions obtained in silico. This efficient screening for new secondary metabolites, performed on 48 gapless genomes revealed total 161 clusters containing nonribosomal peptide...

Since its creation in 2006, Norine remains the unique knowledgebase dedicated to non-ribosomal peptides (NRPs).These secondary metabolites, produced by bacteria and fungi, harbor diverse interesting biological activities (such as antibiotic, antitumor, siderophore or surfactant) directly related diversity of their structures.The team goal is collect NRPs provide tools analyze them efficiently.We have developed a user-friendly interface complete bioinformatics platform.The gathers abundant...

Since its creation in 2006, Norine remains the unique knowledgebase dedicated to non-ribosomal peptides (NRPs). These secondary metabolites, produced by bacteria and fungi, harbor diverse interesting biological activities (such as antibiotic, antitumor, siderophore or surfactant) directly related diversity of their structures. The team goal is collect NRPs provide tools analyze them efficiently. We have developed a user-friendly interface complete bioinformatics platform. gathers abundant...

Natural products and synthetic compounds are a valuable source of new small molecules leading to novel drugs cure diseases. However identifying biologically active is still challenge. In this paper, we introduce activity prediction approach using Bayesian belief network for classification (BBNC). The roots the fragments composing compound. leaves are, on one side, activities predict and, another unknown represented by sets known compounds, inactive also used. We calculated similarity between...

Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks nonribsosomal peptides (NRPs) as such may give insight into origin, biosynthesis bioactivities their constitutive peptides. Hence, structural representation NRPs using monomers provides a biologically interesting skeleton these secondary metabolites. Databases dedicated to Norine, already integrate monomer-based annotations in order facilitate development analysis tools. In this...

Nonribosomal peptides represent a large variety of natural active compounds produced by microorganisms. Due to their specific biosynthesis pathway through assembly lines called NonRibosomal Peptide Synthetases (NRPSs), they often display complex structures with cycles and branches. Moreover contain non proteogenic or modified monomers, such as the D-monomers epimerization. We investigate here some sequence specificities condensation (C) epimerization (E) domains NRPS that can be used predict...

The various bioactivity types and potencies of peptidic natural products (PNPs) are high interest for the development new drugs. In particular, intrinsic antibiotic properties PNPs appear essential to combat antimicrobial resistance that is currently threatening world. first steps in dereplication characterization often involve tandem mass spectrometry (MS/MS). However, such structurally complex peptides challenge interpretation MS/MS results. Only a few software solutions dedicated PNP...

Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there several hundred different monomers that be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently...

Kawal is a fermented food condiment obtained by spontaneous fermentation of Senna obtusifolia leaves. Fermentative microbiota's consists microorganisms producing diversity bioactive molecules. Thus, research novel microbial products capable inhibiting or eliminating plant and pathogens an absolute necessity. In this study, 126 bacterial strains were isolated from Kawal. Phenotypical, biochemical genotypic methods used to determine their genus species. Forty-three (43) them belonging the...

The monomeric composition of polymers is powerful for structure comparison and synthetic biology, among others. Many databases give access to the atomic compounds but often lacking. We have designed a smart algorithm, implemented in tool Smiles2Monomers (s2m), infer efficiently accurately polymer from its chemical structure. Our strategy divided into two steps: first, monomers are mapped on by an efficient subgraph-isomorphism algorithm ; second, best tiling computed so that non-overlapping...

Bacteria and fungi use a set of enzymes called nonribosomal peptide synthetases to provide wide range natural peptides displaying structural biological diversity. So, (NRPs) are the basis for some efficient drugs. While discovering new NRPs is very desirable, process identifying their activity be used as drugs challenge. In this paper, we present novel fingerprint based on monomer composition (MCFP) NRPs. MCFP method obtaining representative description NRP structures from in form....

To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), a dedicated software suite handling refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation easy access to sub-sequences at different levels (cluster, gene,...

Subword composition plays an important role in a lot of analyses sequences. Here we define and study the "local decoding order N sequences," alternative that avoids some drawbacks "subwords length N" approaches while keeping informations about environments sequences ("decoding" is taken here sense hidden Markov modeling, i.e., associating state to all positions sequence). We present algorithm for computing local given set Its complexity linear total (whatever N) both time memory space. In...

The identification of known (dereplication) or unknown nonribosomal peptides (NRPs) produced by microorganisms is a time consuming, expensive, and challenging task where mass spectrometry nuclear magnetic resonance play key role. first step the process always involves establishment molecular formula. Unfortunately, number potential formulae increases significantly with higher masses lower precision their measurements. In present article, we demonstrate that formula assignment can be achieved...

Previous analyses of retroviral nucleotide sequences, suggest a so-called “scrambled duplicative stepwise molecular evolution” (many sectors with successive duplications/deletions short and longer motifs) that could have stemmed from one or several starter tandemly repeated sequence(s). In the present report, we tested this hypothesis by focusing on long terminal repeats (LTRs) (and flanking sequences) 24 human 3 simian immunodeficiency viruses. By using calculation strategy applicable to...