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Pedant-Pro™ Sequence Analysis Suite
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What's new in Pedant version 3.3?
Release Notes (PDF).The Pedant-Pro suite allows a wide range of analysis options:
Pedant-Pro gene report page
The gene report summarizes the most relevant sequence analysis results and provides links to public databases and to various corporate data. Detailed protein characterization includes gene prediction and a detailed characterization of the resulting proteins, based on numerous reliable algorithms. Protein domains are analyzed and potential functions are revealed. Clusters of paralogous proteins are detected. Two- and three-dimensional structural properties are assigned.
The DNA Viewer
The DNA Viewer provides a detailed overview of all structures on the contig. Coding genes and several types of non-coding genes (e.g., for numerous types of RNA) are displayed. The user can browse the contig in freely scalable zoom levels.
The Protein Viewer
The Protein Viewer displays a comprehensive overview of all protein features. Analysis output can be displayed graphically.
Biomax Pathway Viewer
The Pathway Viewer displays enzymes in the relevant pathway context including cross-genome pathway comparison. Metabolic pathways are modeled on the basis of the MetaCat metabolic pathway ontology and the KEGG LIGAND database. The MetaCat metabolic pathway ontology is fully curated by professional experts in the field of biochemistry.
The workflow scheme
The Pedant-Pro software is delivered with standard workflows which have been pre-defined by Biomax. The Pedant-Pro architecture facilitates further integration of customized workflows and additional algorithms. Providing powerful scripting interfaces and Web services interfaces, the Pedant-Pro suite easily integrates into complex computing environments.
Multiple genome comparison
By integrating a specifically constructed database, the Pedant-Pro suite offers different levels of cross-genome comparison.
Positional linkage
Positional linkage provides information about the gene neighborhood and helps to deduce protein functional roles from non-random proximity of genes, usually in operons.
Phylogenetic profiling
Phylogenetic profiling reveals the presence of orthologous gene groups over a specified taxonomic range and provides a taxonomic profile for each protein. This analysis facilitates the prediction of protein function, because similar profiles might indicate similar functionality.
Detailed synteny exploration
Synteny analysis offers detailed comparison of two microbial genomes for contig structure, gene order, homology and indels. The detailed Pedant-Pro gene report is easily available for each of the genes.
Dot-plot overview of syntenic regions of two related genomes
Detailed gene map of a selected syntenic region