Welcome to SCOPE (Suite for Computational identification Of Promoter Elements), an ensemble of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences.
The SCOPE motif finder is designed to identify candidate regulatory DNA motifs from sets of genes that are coordinately regulated. SCOPE motif finder uses an ensemble of three programs behind the scenes to identify different kinds of motifs - BEAM identifies nondegenerate motifs (e.g. ACGTGC), PRISM identifies degenerate motifs (e.g. AWCGRYH), and SPACER identifies bipartite motifs (e.g. ACCNNNNNNNNNGTT). All parameters are automatically set to find the optimal length motif and degree of degeneracy in the reported motifs. To get started, choose a species and an upstream length, then enter a list of gene names (or FASTA sequences) and press the "Run SCOPE" button. For more details, see FAQs and Publications links at the top of the page.
Upload previously emailed WebSCOPE.<job #>.xml.zip or unzipped WebSCOPE.<job #>.xml file:
Species: Upstream sequence: IntergenicFixed Help
Enter gene list or FASTA DNA sequences: Help
- OR -
Upload file with that info:
Examine genome for other genes containing found motif(s)? Help (note: this can take considerable extra time)
Results must include the following motifs: Help
Search:	Plus and minus strands Plus strand only
	Only search for these motifs?
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