Are there any open source, algorithms, or even for-profit software that identifies enhancers, promoters, and other functional elements in a genome? I tried looking around but I found databases with this information and research articles, but no specific software that I can see.
You have not mentioned which organism of genome your are working on. Anyway,here the list mainly on promoter prediction
Easy promoter Prediction Program (EP3): http://bioinformatics.psb.ugent.be/webtools/ep3/
Prediction of promoter regions from genomatix: http://www.genomatix.de/online_help/help_gems/PromoterInspector_help.html
Berkely promter prediction(both prokaryote & eurkaryote): http://www.fruitfly.org/seq_tools/promoter.html
McPromter: http://tools.genome.duke.edu/generegulation/McPromoter/
Promter prediction server: http://www.cbs.dtu.dk/services/Promoter/
Human, Mouse and Rat promoter extraction service: http://biowulf.bu.edu/zlab/PromoSer/
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