Promoter alignment

Pro-Coffee is designed for aligning non-coding regions containing transcription factor binding sites (TFBS). It uses a substitution matrix estimated on TRANSFAC multiple sequence alignments of TFBS. The following two examples illustrate its usage:
The current version of Pro-Coffee uses a default gap-opening penalty (GOP) of -40 and a gap-extension penalty (GEP) of 0. Yet, our benchmarks suggest that good alignments are obtained using GEP values of 0 or -1 and a GOP value between -20 and -50. It may therefore be advisable to explore this range of values when computing an alignment. One can do so using the following command, where @EP stands for Extra Parameters:

t_coffee -seq<your_seq> -method promo_pair@EP@GOP-40@GEP0 -extend_seq
Subpages (2): c18orf19 IL5