MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Table 1 Definition of positive and negative sets of matrix matches

Criterion	Gal4p	Rpn4p
Unique specificity	Spacer of 11 bp [50]	Atypical zinc finger [42]
Well characterized specificity	Protein-DNA co-crystal [51]	Large number of binding sites, low degeneracy [42]
Well characterized target gene set	Classic genetic system [52] and high-throughput studies [45,46]	Targets include almost all proteasomal subunits [42] stereotypical expression pattern [48]

Criteria used to define positive and negative sets to use in this study. It is important to avoid factors whose specificity overlaps with other factors, because binding sites that are not occupied by one factor may be constrained because of binding by another, and to choose factors with characterized specificity because our methods rely on the assumption that the specificity is known.

ISSN: 1474-760X