MatrixGen

MatrixGen is an excellent Bioinformatics application that assists in generating scoring matrices from aligned Amino Acid and DNA datasets. The primary use of these matrices is to generate more precise and accurate alignments through Clustal. Although there are many algorithms and programs for protein alignment and similarity determination, MatrixGen stands out in its unique features. It is not an alignment program by itself but is designed to interoperate with such programs and enhance the accuracy of alignments.

Multiple techniques for protein alignment rely on a weighted matrix for scoring the possibility of transitions from one amino acid to another. The alignment with the highest score is considered the most accurate, and these matrices are created by analyzing previously aligned sets of proteins. The probabilities of mutation in an evolutionary context are used to calculate these weighted matrices, which are mostly presented as a log of odds (lod) matrix.

MatrixGen accurately and efficiently calculates these probabilities as described by Henikoff and Henikoff, but it does not do block clustering as explained by the same paper. The primary objective of MatrixGen is to create a matrix explicitly for the protein being aligned using a dataset of closely related proteins. Additionally, MatrixGen generates distance matrices and other useful statistics about the dataset.

Overall, MatrixGen is a powerful tool that fulfills its primary purpose of generating scoring matrices for aligned Amino Acid and DNA datasets. It substantially enhances the accuracy of alignments by interooperating with Clustal and providing unique functionalities.