Table 1 Examples of hierarchical model building in C4. Instead of building each model from scratch, most models are created in a modular fashion by making adaptions and additions to other models. This facilitates the building of complex models.
From: Automated generation of heuristics for biological sequence comparison
| Model | Components | States | Transitions |
|---|---|---|---|
| ungapped | substitution matrix | 3 | 3 |
| Needleman-Wunsch (NW) | ungapped with gap penalties | 3 | 5 |
| Smith-Waterman (SW) | NW + local alignment scope | 3 | 5 |
| Smith-Waterman-Gotoh (SWG) | SW + affine gap costs | 5 | 9 |
| est2genome | SWG + intron models | 10 | 24 |
| protein2dna | SWG + translation + frameshifts | 6 | 13 |
| protein2genome | p2d + intron model | 13 | 33 |
