Analysis of TRANSFAC binding sites. Realignment of sequences used within TRANSFAC to define PWMs which incorporate optional gaps. Left: An alignment, a standard PWM and a gapped PWM for the monomer transcription factor MEF-2. Additional gaps improve the alignment right across the motif, especially the well conserved TA motif that is not apparent in the ungapped alignment. Right: An alignment, a standard PWM and a gapped PWM for the homodimer transcription factor POU. Additional gaps improve the alignment of the conserved ATA and TTA motifs. The realignments show a significant proportion of sites both with and without gaps. The upper logos show the original TRANSFAC motifs and their information content in bits (see Methods for the details of the calculation). The lower logos show the motifs after the addition of gaps, indicated by the percentage of sequences where a nucleotide is present.
Reid et al. BMC Genomics 2010 11:30 doi:10.1186/1471-2164-11-30