Skip to main content

Table 1 Comparison to related works. ComPath is compared with five existing pathway analysis systems: The SEED, Pathway Tools, KAAS, KOBAS, and Path-A.

From: ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts

System ComPath The SEED Pathway Tools KASS KOBAS Path-A
Focus More interactive interface, more data integration Annotation by EC, RC, and GO Genomic data integration, pathway prediction and annotation Simple gene annotation using KO Annotation by KO with statistical evaluation Annotation against model pathway
Reference Pathway Database KEGG Subsystems De novo generation by PathoLogic algorithm KEGG KEGG 10 model pathways – spanning 125 organism-specific pathway instances
Classifier FASTA Whole-HMM CSR-HMM PDB-domain search BLAST PathoLogic BLAST-BBH BLAST-SBH BLAST Opt HMM BLAST-HMM BLAST Motif SVM HMM
Ontology EC, GO EC, RC, GO Pathway Tools Ontology, EC KO KO EC
Sequence analysis CDD search, Prosite pattern search, phylogenetic tree analysis, BAG sequence clustering, Gibbs motif sampling, iGibbs Gene cluster search, Phylogenetic tree analysis No No No No
Pathway representaion Automatic generation based on information in KEGG/KGML KEGG map Automatic generation based on MetaCyc database KEGG map KEGG map KEGG map
Genome context CGView, Gene cluster search GBrowse, Gene cluster search Genome browser at BioCyc site No No No
Data management Yes Yes Yes Yes Yes Yes