Dcode.org: Tools Developed by the Research Group of Ivan Ovcharenko at the National Library of Medicine

 Dcode.org   ECR Browser   Mulan   zPicture   DiRE   SynoR   rVista 2.0   multiTF   SNPDelScore 

 Causal noncoding variants
SNPDelScore -- Combining multiple methods developed by the community to predict causal noncoding variants.
CAPE -- Predicting causal noncoding variants.

 Regulation of co-expressed genes
CLARE -- Prediction of regulatory motifs and motif combinations in a set of co-functional enhancers.
DiRE -- Identification of proximal and Distant Regulatory Elements of co-regulated genes.
SynoR -- Prediction of synonymous regulatory elements in vertebrate genomes.

 Whole genome alignments
ECR Browser -- Evolutionary conservation of multiple genomes. Identification and sequence analysis of regulatory elements.
Genome Alignment in ECR Browser -- Align your FASTA nucleotide sequence to a genome of choice.

 Multiple and pairwise sequence alignments
Mulan -- Full multiple sequence alignment. [Interactive conservation profiles, phylogenetic trees, etc.]
zPicture -- Stacked pairwise and multiple sequence alignment.

 Identification of conserved transcription factor binding sites (cTFBS)
Excluding up to 95% false positive TFBS predictions using sequence conservation as a filter.
multiTF -- cTFBS in multiple sequence alignments.
rVista 2.0 -- cTFBS in pairwise alignments.