WordSpy -- identifying transcription factor binding motifs by building a dictionary and learning a grammar

What you can do:
Identify transcription factor binding sites or other meaningful DNA motifs.
Highlights:
  • One significant feature of WordSpy is the combination of a word counting method and a statistical model which consists of a dictionary of motifs and a grammar specifying their usage.
  • The algorithm is suitable for genome-wide motif finding; it is capable of discovering hundreds of motifs from a large set of promoters in a single run.
  • WordSpy is enhanced by applying gene expression information to separate true TFBMs from spurious ones, and by incorporating negative sequences to identify discriminative motifs.
  • In addition, the author also use randomly selected promoters from the genome to evaluate the significance of the discovered motifs.
  • The output from WordSpy consists of an ordered list of putative motifs and a set of regulatory sequences with motif binding sites highlighted.
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
  • DNA sequence analysis tool
  • promoter analysis tool
  • promoter elements prediction tool
  • transcription factors
  • response elements
  • cis-elements
  • cis-regulatory modules analysis tool
  • DNA motif prediction tool
This record last updated: 11-18-2005
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