Table 2:
Current list of commonly used publicly available pipelines for the functional annotation of metagenomic data sets
| Pipeline/tools | IMG/M | METAREP | CAMERA | RAMMCAP | MG-RAST | Smash community | MEGAN4 | CoMet | WebMGA |
|---|---|---|---|---|---|---|---|---|---|
| Functional analysis | |||||||||
| Homology-based | |||||||||
| Known sequence | NCBI (NR), SMART, UniProt | NCBI (NR), UniProt | NCBI (NR) | – | NCBI (NR), SMART, UniProt | SMART, UniProt | NCBI (NR) | – | NCBI (NR) |
| Metagenomic data sets | IMG/M | – | – | – | IMG/M | – | – | – | – |
| Orthologous groups | COGs | – | COGs | COGs | COGs, eggNOGs | COGs, eggNOGs | – | – | COGs |
| Protein families | Pfam, TIGRfam | Pfam, TIGRfam | Pfam, TIGRfam | Pfam, TIGRfam | FIGfams | Pfam | – | Pfam | Pfam, TIGRfam |
| Ontology | GO | GO | GO | GO | GO | – | – | GO | GO |
| Enzymes, pathways and subsystems | KEGG, SEED | PRIAM | KEGG, SEED | – | KEGG, SEED | KEGG | KEGG, SEED | – | KEGG |
| Protein interactions | – | – | – | – | STRING | STRING | – | – | – |
| Motif- and pattern-based | |||||||||
| Database | InterPro | – | – | – | – | – | – | – | – |
| Context-based | |||||||||
| Approach | Gene neighborhood | – | – | – | – | Gene Neighborhood | – | – | – |
| Other functional analysis | |||||||||
| Types of predictions | CRISPRs, enzymes, transporter classes | Enzymes, transmembrane helices, lipoprotein motifs | – | – | – | Protein networks | – | – | – |
| URL | http://img.jgi.doe.gov/m/doc/uiMap.html | http://www.jcvi.org/metarep/ | http://camera.calit2.net/ | – | http://metagenomics.nmpdr.org/ | http://www.bork.embl.de/software/smash/ | http://ab.inf.uni-tuebingen.de/software/megan/ | http://comet .gobics.de/ | http://weizhong-lab.ucsd.edu/metagenomic-analysis/ |
| References | [26] | [27] | [28] | [29] | [30] | [31] | [32] | [33] | [34] |