Table 1.

Comparative genomics data to infer functionally significant regulatory elements

Program	Mechanisms	Target Regulatory Elements	URL
fitCons	Compares the selective pressure consequences to indicate potential for genomic function	Any Non-Coding Genetic Variant	http://compgen.cshl.edu/fitCons/
GERP++	Compares p-values in order to predict genetic conservation in terms of rejected substitution (RS), which is the difference between neutral rates of substitution and the observed rate as estimated by maximum likelihood .	TF Binding Sites, Promoters, Enhancers, Silencers	http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html
Phastcons/PhyoP	Computes conservation or acceleration p-values based on alignments with respect to a neutral model of evolution	TF Binding Sites, Promoters, Enhancers, Silencers	http://compgen.cshl.edu/phast/index.php
SiPHY	Models biased nucleotide substitutions and characterizes substitution patterns from sequence alignments	TF Binding Sites, Promoters, Enhancers, Silencers	http://portals.broadinstitute.org/genome_bio/siphy/
dbPSHP	Combines data from over 15,000 loci from publications and 15 statistical terms to identify genetic regions with potential positive selection	Any Single Nucleotide Variant	http://jjwanglab.org/dbpshp