Table 1.
Non-exhaustive summary table of existing functional annotation programs or pipelines.
| Program/Pipeline | Installation | Used Software | Datasets | Comments |
|---|---|---|---|---|
| Blast2GO [20] | Local installation and web/cloud services | BLAST+, Interproscan, BLAST2GO specific software, etc. | Custom, Normally, NCBI BLAST DBs, InterPro, GO | Subscription tool. Visualization dashboard. Gene structural annotation options. Newer versions integrated into other toolboxes. |
| eggNOG mapper [9] | Web service and local installation | DIAMOND, HMMER | eggNOGdb (from several sources), GO, PFAM, SMART, COG | Available command-line tool and REST API for querying the service. Gene structural annotation options. |
| FA-nf | Local installation | BLAST+, DIAMOND, Interproscan, KOFAM, CDD, SignalP, TargetP, etc. | Custom. Normally, NCBI BLAST DBs, InterPro and UniProt-GOA | Based on Nextflow pipeline framework and software containers. |
| GenSAS [15] | Web service | BLAST+, DIAMOND, Interproscan, SignalP, TargetP, etc. | SwissProt/TrEMBL, RefSeq, RepBase | No installation needed. Requires web user registration. Includes gene structural annotation and visualization. There can be resources and usage restrictions. |
| MicrobeAnnotator [18] | Local installation | BLAST+, DIAMOND, KOFAM. | SwissProt/TrEMBL, RefSeq, KEGG | Focused on microbiomes. Conda/Python based. |
| PANNZER2 [17] | Web service | SANSparallel | UniProt, UniProt-GOA, GO, KEGG | Available command-line tool for querying the service. |
| Sma3s [19] | Local installation | BLAST+ | Reference datasets generated from UniProt, GO | A Perl script. Simple installation. |