What is the best computational method for predicting regulatory elements in the pig genome? I have a list of differentially expressed genes as determined by RNA-Seq in 3 different tissues and I would like to narrow down on some candidate regulatory regions for DNA methylation analysis (my hypothesis is that differences in transcript abundance can be explained by differences in methylation status at their respective promoter or enhancer sites).
I have tried BLASTing the human sequences found in DNase hypersensitive sites (found at the regulatory elements database: http://dnase.genome.duke.edu/index.php) against the pig genome, but I end up getting hits all over the genome (the idea here is that regulatory elements should not be packaged as tightly, so more accessible to DNase). The hits that show up on the same chromosome as the gene end up having E values greater than 1.
Any suggestions would be greatly appreciated!