Regulation of co-expressed genes
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 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.
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Whole genome alignments
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 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.
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Multiple and pairwise sequence alignments
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 Mulan -- Full multiple sequence alignment. [Interactive conservation profiles, phylogenetic trees, etc.]
zPicture -- Stacked pairwise and multiple sequence alignment.
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Identification of conserved transcription factor binding sites (cTFBS)
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 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.
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