A program to find regions of similarity between homologous protein sequences using dotmatrix analysis |
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| Affiliation: | 1. Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands;2. Department of Biology and Biotechnology, University of Pavia, Pavia, Italy;1. Department of Veterinary Surgery, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China;2. College of Animal Science and Technology, Northeast Agricultural University, Harbin, China;3. Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, China;1. Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand;2. Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand;3. School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand |
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| Abstract: | MATRIX is a program designed primarily to enable the user to visualize all regions of similarity between two proteins at a glance. The program helps the user to see where they are similar—at what relative positions in the amino acid sequences of the two proteins in question does the similarity exist; how they are similar—what functional characteristics the two similar sequences have in common; and to what extent they are similar—is the similarity significant, if so how significant relative to other similar sequences in the protein. This is achieved by constructing a diagram in which quantitative parameters of amino acids are used to compare every amino acid residue of the first protein with every amino acid residue of the second.Another function of the program is, given two sets of atomic coordinates—either of different proteins or for the same protein (for self-comparison)—to demonstrate which residues of the two proteins, when the two proteins are superimposed upon each other, appear in the same space (or are close to each other). |
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