Flowchart of the proposed method. (a) The target genes and consensus of transcription factors in the three sensu stricto species (S. cerevisiae, S. paradoxus and S. mikatae) were downloaded from the MYBS database; (b) nucleosome positions in S. cerevisiae was compiled from Mavrich et al. ; (c) orthologous genes were collected from OrthoMCL-DB and detected S. cerevisiae specific genes; (d) duplicate gene pairs were identified in S. cerevisiae; (e) the frequency distribution of TFBSs in orthologous genes, sacharomyces specific genes and duplicate gene pairs were derived with respect to nucleosome occupancy in S. cerevisiae; (f) suitable statistical tests were used to determine if the distributions in (e) was significantly different; (g) the evolutionary rates of TFBS present in sensu stricto yeasts was calculated at NRs and NDRs; and (h) the difference in (g) were tested for significant difference.
Swamy et al. BMC Evolutionary Biology 2011 11:150 doi:10.1186/1471-2148-11-150