Sequence Alignments With Primary and Secondary Structure Analysis

Improving Sequence Alignments With Primary and Secondary Structure Analysis 

The primary structure of a protein contains information of use to homology modelers. A primary structure analysis can be used to predict ot-helical or 

Hydropathy plots are used to predict buried and exposed regions of a protein. Use of these plots was first demonstrated by Rose and Rose and Roy. Hydropathy plots are based on Chothia s observation that hydro-phobic residues (amino acid residues with hydrophobic sidechains) tend to be buried when the protein exists in its native conformation. More than one set of hydropathy values is available. The best known hydropathy indexing methodology is that of Kyte and Doolittle. 

There are two methods of varying the weight of the residues linear or exponential. The default method of performing a hydropathy plot assumes that each residue is equally important, which thus produces a weight of 100%. 

Pattern and Motif-Based Secondary Structure Prediction 

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