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Researchers at Iowa State University have developed a new amino acid substitution matrix, SeqStruct, that takes into account both the sequence and structure data of the protein in the sequence matching procedure. This allows for better sequence matching scores across diverse proteins, especially for those proteins whose structures are similar but whose sequences are not.

 

Protein sequence matching has a wide variety of uses in biology. For example, it is important in determining whether regions of similarity in proteins are a result of evolutionary or functional relationships, and improvements in sequence matching will allow for better gene annotations and protein modeling. Along with protein sequences, protein structures also contain important information about the protein, but many commonly used amino acid substitution matrices, such as BLOSUM62, do not take this important structural information into account. However, SeqStruct does incorporate such structural information into its algorithm, and when combined additively with the BLOSUM62 matrix, leads to improved sequence matching scores and homology detection when compared to traditional similarity matrices and single structure-based matrices. SeqStruct also allows for improved discrimination between proteins that are distant homologs and those that are dissimilar in structure. Overall, the use of SeqStruct leads to major improvements in sequence matching across various different proteins.

• Easy implementation as a result of the use of a simple 20x20 amino acid similarity matrix

• Significant improvements in sequence similarity and gap reduction when compared to BLOSUM62

• Easy implementation as a result of the use of a simple 20x20 amino acid similarity matrix

SeqStruct provides improved protein sequencing and identification of protein function. It also has many uses in the bioinformatics industry.