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NCBI DCODE.org Comparative Genomics Developments is a publicly available resource for regulatory genome data mining. It provides tools for evolutionary comparisons, sequence alignments, and detection of functional sequence patterns.
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| News |
April 30, 2008
The DiRE tool operates with new ECR Browser alignments now. It is also possible to run DiRE on human (hg18), mouse (mm9), and rat (rn4) genomes.
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| 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.
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| 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.
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| Regulation of co-expressed genes |
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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| 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.
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