When citing this work, please cite the following papers:
The Helix-Turn-Helix (HTH) motif is one of the best studied motifs in proteins. Proteins with such motif are usually transcription factors. They bind to DNA and affect the function of RNA polymerase, thus regulating the gene expression. It is found that the HTH motif of these proteins are responsible for binding with DNA.
Detecting motifs including HTH motif has become an important issue in biochemistry. The most widely used methods are statistically based profile methods, with Dodd & Egan (DE) method being the most popular used for detecting HTH motif. This thesis implemented the GYM algorithm based on pattern discovery techniques. The program also gives some comparisons on these two methods.
Here are some protein
families you can test:
AraC, LysR, Sigma, Reg, and Negate.
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