FirstEF - first-exon and promoter prediction program for human DNA.
Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms.
WWW Promoter Scan. Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.
CpG Island Explorer CpG Island Explorer is aimed at CpG island searching. A specific feature of this program is that a file containing multiple DNA sequences in FASTA or GB format can be processed in one operation.
CpGProD - CpG Island Promoter Detection. a program dedicated to the prediction of promoters associated with CpG islands (CGIs) in mammalian genomic sequences.
DNA Analytics Software from Agilent Technologies. DNA Analytics 4.0 provides an intuitive user interface for visually exploring, detecting, and analyzing CGH, ChIP, and Methylation data in context with the genome of interest.
EpiDesigner EpiDesigner is a tool for designing quantitative DNA methylation experiments for Sequenom's EpiTYPER technology. Link only.
MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers. Currently, it can design primers for two types of bisulfite PCR: 1) Methylation-Specific PCR (MSP) and 2) Bisulfite-Sequencing PCR (BSP) or Bisulfite-Restriction PCR.
MethTools a toolbox to visualize and analyze DNA methylation data.
Pyro Q-CpG from QIAGEN quantification of DNA methylation using pyrosequencing. Link only.