Please note that SCOPE, as well as its datasets, are no longer updated, supported or developed. The SCOPE web-application has been permanently decommissioned as of July 1, 2016. The sourcecode, JavaDoc and executables are available for download on the About page.

Dartmouth College SCOPE Version 2.1.0

About SCOPE...

SCOPE is a novel parameter-free method for de novo computational motif discovery, designed for biologists. The only inputs required by SCOPE are a set of unaligned sequences and a species designation. SCOPE utilizes three algorithms to identify sequence motifs: BEAM finds non-degenerate motifs, PRISM finds degenerate motifs, and SPACER finds bipartite motifs. Results from all three algorithms are merged and the best scoring motifs are presented.

In tests on 78 sets of coregulated genes with experimentally determined binding sites, SCOPE identified motifs (of previously unknown length, degree of degeneracy and orientation) with a high level of accuracy. Ten other motif-finding programs with web-based interfaces were also run on this dataset for comparison, and SCOPE was found to be more accurate than all of them. SCOPE is also extremely robust to noise in input datasets (for details see our SCOPE paper: Chakravarty et al., 2006 submitted). In semi-synthetic test regulons where four times as many random sequences as bona fide upstream sequences were present, SCOPE's performance degraded by only 21%, thus SCOPE is able to predict transcription factor binding sites with a high level of accuracy. 

SCOPE accepts genes for analysis either as FASTA sequences or as gene names, and is currently configured for the analysis of a number of prokaryotic and eukaryotic genomes. Run times for SCOPE are fast (in the order of one to five minutes), and output consists of the significance score, the location, count, and identity (consensus sequence and PWM) of all statistically significant motifs. Users may modify the output of SCOPE to individually view the most significant motifs from each of its component algorithms and view maps of the locations of each of the motifs in the set of genes examined.

We believe the SCOPE web server is a practical resource for members of the biological community with an interest in computational motif-finding.

Availability and Requirements

  • Project name: SCOPE
  • Project home page:
  • Operating system(s): Platform independent
  • Programming language: Java
  • Other requirements: Java 1.5 or higher
  • License: Free for academic use, non-academic restrictions
  • Sourcecode, JavaDoc and executables are available here.