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
Literature & Tutorials:
This record last updated: 11-18-2005