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.

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


Slater and Birney BMC Bioinformatics 2005 6:31   doi:10.1186/1471-2105-6-31

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