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

 Dcode.org   ECR Browser   ECRBase   Mulan   zPicture   DiRE   SynoR   rVista 2.0   multiTF   eShadow   CAPE   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.
eShadow -- Phylogenetic shadowing of closely related species.

 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.