Metabolic Pathway Builder

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract Metabolic Pathway Builder is a software and data platform for fast, accurate annotation & comparative genomic and metabolic analysis of multiple organisms.

Metabolic Pathway Builder software enables you to generate maximum knowledge from your data: conduct complete analyses from sequences to the metabolic reactions and pathways involved, both comparatively (between multiple organisms) and differentially (using gene expression data).

Metabolic Pathway Builder Features/Capabilities:

1) Visualizers and tools for data manipulation --

• a) Visualize multiple strains or organisms simultaneously on maps;
• b) Visualize chromosomes and plasmids on linear and circular genomic maps;
• c) Synchronize and zoom to link maps and focus on areas of interest between organisms or strains;
• d) Show genomic features on maps (CDS, tRNAs, rRNAs, signals, GC content and skew, etc.);
• e) Visualize the metabolic reactions & pathways in which organism and strain specific genes are implicated;
• f) View, sort, filter and export data tables; and
• g) Visualize and identify specific, common and complementary pathways or sub-pathways between organisms.

2) Functional annotation --

• a) Predict & confirm ORFs, coding sequences (CDSs);
• b) Transfer annotations between CDS;
• c) Detect frame shifts;
• d) Predict and find Pfam domains;
• e) Identify and locate transmembrane regions, antigenic sites, and protein secondary structures (EMBOSS methods);
• f) Identify conserved regulatory regions;
• g) Predict RNA location;
• h) Predict & confirm EC numbers on a set of genes; and
• i) Add specific identifiers, notes, comments and citations to the genomic features in your data.

3) Comparative annotation --

• a) Map and assemble contigs to obtain a complete sequence
• b) Compute and visualize SNPs and DIPs -

• 1) Calculate SNPs and DIPs on contigs & on mapping results; and
• 2) Visualize SNPs and DIPs in tables and on synchronized sequence maps.

• c) Compare complete sequences or sets of contigs between multiple genomes;
• d) Identify species or strain-specific genes and visualize them on genomic maps;
• e) Identify genes/CDS that are common to all known strains of a given organism and visualize them on genomic maps;
• f) Extensive BLAST options;
• g) Visualize and compare specific, common or complementary pathways between organisms;
• h) Identify compounds that are only present in a specific species or common to several strains or species;
• i) Identify reactions that are -

• 1) Specific to a given organism; and
• 2) Common to several strains or species; and

• j) Find syntenies -

• 1) Identify and compare groups of homologous genes; and
• 2) Detect chromosomal reorganization between genomes & phylogenetically-related strains.

4) Metabolic pathway analysis and exploration --

• a) Predict protein functions and enzymatic activity;
• b) Identify and visualize metabolic reactions & pathways in which organism and strain specific genes are implicated;
• c) Find and visualize targeted metabolic pathways using chemical structure searches;
• d) Identify and visualize specific, common and complementary pathways or sub-pathways between organisms;
• e) Predict and identify conserved regulatory regions; and
• f) Identify, compare and visualize groups of homologous genes and explore the organization of operons and syntenies.

5) Alignment and phylogeny --

• a) ClustalW;
• b) Muscle, MAFT; and
• c) Build phylogenetic trees - BIONJ, NJ, UPGMA.

6) Blast and databank searching --

• a) Blast - local or distant (BlastN, BlastX, BlastP, tBlastN, tBlastX, psiBlast);
• b) Local or public databank searches - UniProt, Genbank, customized, and in-house databanks;
• c) Select and add annotations to your local Blast databanks; and
• d) Store databanks on your desktop or in a shared directory.

The Metabolic Pathway Builder software and data platform also includes:

GenoAnnot-ProteoAnnot -- Your integrated annotation pipeline --

Simplify, automate and accelerate your nucleic and proteic annotation using Genostar’s streamlined pipeline.

GenoAnnot-ProteoAnnot connects and integrates the many methods and tasks necessary for rapid, in-depth annotation and provides you with user-friendly visualizers and tools for sequence manipulation.

The manufacturer's versatile design automatically handles different data formats and leaves you free to concentrate on your research.

With GenoAnnot-ProteoAnnot you can easily annotate complete or partial sequences, identify specific coding regions, transfer annotations, and map contigs on a reference sequence to assemble your complete sequence.

Focus on and explore specific regions in depth. Automate your standard annotation procedures.

PathwayExplorer -- to explore the relationships between genes, their enzymatic products, and metabolic pathways catalyzed by these enzymes, including computing and querying homologies among CDSs.

PathwayExplorer gives you the capability to:

1) Compare several genomes.

2) Search for the genes that are specific to one of them.

3) Identify the corresponding specific reactions and pathways on metabolic maps.

4) Search for all the reactions which result in the chemical compounds described by the structure they share.

5) Then, track back to the genes whose products catalyze these reactions.

Use PathwayExplorer with MicroB (see below...) or a customized data set --

1) Integrated and classified genomic and post-genomic data for either 10-50, or nearly 700 genomes;

2) Metabolic pathway entries with information about metabolites, reactions, and corresponding enzymatic function;

3) Over 7,000 metabolic pathways, each connected to larger functional networks; and

4) 120 metabolic networks total - amino acid metabolism, lipid metabolism, energy metabolism, and others.

Or, use PathwayExplorer with BacDat datasets - With genomes or organisms of specific interest to your research.

MicroB - MicroB is a relational database that integrates and connects the most recent genomic, proteic, biochemical and metabolic reference data available on 1,250 complete microorganisms. It enables comparative analysis of your data in their functional context.

Note: See G6G Abstract Number 20152R for additional product info from this manufacturer.

System Requirements

Contact manufacturer.

Manufacturer

• Genostar
• Home office: 78 bis, avenue Henri Martin, 75116 Paris France
• Sales / Service / Research & Development Group:
• 60 rue Lavoisier, 38330 Montbonnot France
• Tel. +33 4 76 97 10 70
• E-mail: info@genostar.com

Manufacturer Web Site Metabolic Pathway Builder

Price Contact manufacturer.

G6G Abstract Number 20151R

G6G Manufacturer Number 101123