Metabolic Pathway Builder Features

 

Visualizers and tools for data manipulation

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

 

Functional annotation

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

 

Comparative annotation

• Map and assemble contigs to obtain a complete sequence
• Compute and visualize SNPs & DIPs

             - Calculate SNPs and DIPs on contigs & on mapping results
             - Visualize SNPs and DIPs in tables and on synchronized sequence maps

• Compare complete sequences or sets of contigs between multiple genomes
• Identify species or strain-specific genes and visualize on genomic maps
• Identify genes/CDS that are common to all known strains of a given organism and visualize on genomic maps
• Extensive Blast options
• Visualize and compare specific, common or complementary pathways between organisms
• Identify compounds that are only present in a specific species or common to several strains or species.
• Identify reactions that are:

             - Specific to a given organism

             - Common to several strains or species

• Find syntenies:

             - Identify and compare groups of homologous genes

             - Detect chromosomal reorganization between genomes & phylogenetically-related strains

 

Metabolic pathway analysis and exploration

• Predict protein functions and enzymatic activity
• Identify and visualize metabolic reactions & pathways in which organism and strain specific genes are implicated
• Find and visualize targeted metabolic pathways using chemical structure searches
• Identify and visualize specific, common and complementary pathways or sub-pathways between organisms
• Predict and identify conserved regulatory regions
• Identify, compare and visualize groups of homologous genes Explore organization of operons and syntenies

 

Alignment and phylogeny

• ClustalW
• Muscle, MAFT
• Build phylogenetic trees: BIONJ, NJ, UPGMA

 

Blast and databank searching

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