GenomeTrafac -- a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
What you can do:
Use comparative genomics approach to characterize gene models and identify putative cis-regulatory regions of RefSeq Gene Orthologs.
Highlights:
- This database allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes.
- Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures.
- The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures.
- It is designed to perform the following tasks:
- *Find conserved cis-element clusters within BlastZ-identified conserved sequence alignment blocks.
- *Find shared cis-elements between user-selected gene segment pairs.
- *Genome-wide ortholog conserved Cis-element module search
Keywords:
- transcription factor binding site prediction tool
- transcription factor binding site analysis tool
- DNA-binding sites prediction tool
- cis-elements prediction tool
- cis-regulatory elements prediction tool
- promoter analysis tool
- promoter elements prediction tool
- combinational cis-regulatory elements
- transcription factors
- response elements
- cis-elements
- cis-regulatory modules analysis tool
- cis-clusters
- microRNA gene promoter
- gene models
- complex cis-element structures
- human transcription factor binding sites
- mouse transcription factor binding sites
This record last updated: 03-21-2007