Hydrophobic Domain Detection

Objective: Detect hydrophobic domains in multiple sequences in a Q-fasta file.

For gene discovery, those genes encoding transmembrane proteins are traditionally favorite targets of many research organizations primarily because transmembrane proteins consist of several important gene families such as G-protein coupled receptors, the so called seven transmembrane proteins, channel proteins, adhesion molecules and so on. Transmembrane proteins play critical roles in cellular processes and are often disease-related. Localized on the cell membrane, they are ideal targets of designed drugs. The fact that transmembrane proteins have at least one unusual long stretch of hydrophobic residues (about 20 amino residues) makes it possible to predict transmembrane domains with high accuracy.

The hydrophobic domain prediction function in the package is written based on the method described by Kyte and Doolittle. It continually takes the average hydropath of a predefined length of a moving segment. A region with a hydropath value above a certain threshold will be considered as a transmembrane domain. It is very effective for screening potential transmembrane proteins.

Features:

1. Detect hydrophobic domains in multiple sequences.
2. Accept both nucleotide and protein sequences.
3. Adjustable parameter settings.
4. Instant data report: provide the total number of predicted transmembrane domains and average hydropaths and locations of all detected hydrophobic domains in each sequence.