Detecting Helix-Turn-Helix motifs in Proteins

GYM 2.0 can be used to detect Helix-Turn-Helix Motifs in protein sequences.

When citing this work, please cite the following papers:

G. Narasimhan, C. Bu, Y. Gao, X. Wang, N. Xu, K. Mathee, Mining for Motifs in Protein Sequences, J. of Computational Biology, 9(5):707-720, 2002.
Y. Gao, K. Mathee, G. Narasimhan, X. Wang, Motif Detection in Protein Sequences, Proc. of the 6th SPIRE Conference, 63-72, 1999.

For using this program, please enter the protein sequence in the text area.

If you use the GYM 2.0 program in your research, please cite the papers listed above.

Please copy and paste the sequence in the text area.
(No spaces or end of line characters).

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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