fREDUCE

fREDUCE detects putative regulatory motifs by correlation of sequence with expression data. fREDUCE enables the search of degenerate motifs containing IUPAC characters representing multiple base pairs:
  • 2-fold IUPAC characters: R = A/G; Y = C/T; M = C/A; K = T/G; W = T/A; S = C/G
  • 3-fold IUPAC characters: B = C/T/G; D = A/T/G; H = A/T/C; V = A/C/G
1. Please choose an expression data file on your local file system (sample input file): Expression File:
2. Search Yeast Promoter Sequence?(if yes, no sequence file is required): yes, no
3. Sequence file (from which to search the motifs, in FASTA format): Sequence File:
4. Allowed IUPAC characters: 2 fold only, all
5. Maximum motif length:
6. Maximum number of IUPAC substitutions:
7. Search the reverse complement: yes, no
8. If you search for motifs longer than 8bps or with more than 1 IUPAC substitution, the results will be sent to you by email. email address:

retype email:
9. Description of the submitted expression data (Optional, but will help to identify your search):

References:

  • Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet. 2001, 27:167-71.
  • Wu RZ, Chaivorapol C, Zheng J, Li H, Liang S: fREDUCE: Detection of degenerate regulatory elements using correlation with expression. BMC Bioinformatics 2007, 8:399.
©copyright: Hao Li Lab 2007
(Last updated: Jan 16, 2009)