Table 1.
Running times per gigabase of sequence data on a single 2 GHz processor
| Tool | Method | Symbol | Ref. | Time/Gbase |
|---|---|---|---|---|
| FragGeneScan |
Hidden Markov Model |
FGS3,FGS5 |
[11] |
6 hours |
| MetaGeneAnnotator |
Codon usage + start site heuristics |
MGA |
[9] |
15 min |
| MetaGeneMark |
Codon usage + gc-content heuristics |
MGM |
[8] |
20 min |
| Orphelia |
Neural network |
OPH |
[10] |
13 hours |
| Prodigal | Codon usage + dynamic programming | PRD | [12] | 30 min |
Compared with downstream analyses, ab initio gene calling is computationally inexpensive.