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 |