Free and open source Bioinformatics application that will help you generate scoring matrices
Version: Nov 2008MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments.
Operating System: Mac OS X
There are many algorithms for determining protein similarity and aligning proteins. There are also many programs for doing this. MatrixGen is not an alignment program. It does, however, interoperate with alignment programs to provide a more accurate alignment.
Many methods for aligning proteins rely upon a weighted matrix to score the likelihood of transitions from one amino acid to the next. The alignment with the highest score is then judged the most correct alignment.
These weighted matrices are generated by easily analyzing previously aligned sets of proteins to be able to determine the probability of mutation of a particular Amino Acid in an evolutionary context.
These matrices are most generally presented as a log of odds (lod) Matrix. Each element of a lod Matrix is the logarithm of a ratio of probabilities. Specifically, the probabilities considered are the observed probability of a pair of amino acids over the expected probability of a pair of amino acids.
MatrixGen calculates these probabilities as described by Henikoff and Henikoff. MatrixGen does not do block clustering as described by this same paper. The idea behind MatrixGen is to create a matrix specifically for the protein that you are aligning using a dataset of very similar proteins. Matrixgen will also generate distance matrices and give you other useful statistics about your dataset.