Matrix Editor is an application used for matrices inspection and customization for Vector NTI’s AlignX (An advanced application that is used for simultaneous alignment of nucleotide and amino acid sequences) and AlignX Blocks (An advanced application for searching, analyzing and modifying blocks of protein sequences). It was initially developed by InforMax Inc. It is a miscellaneous tool included in the Vector NTI software.
Matrices are generated from assigned scores. These scores came from evaluating pairwise sequence alignment or based from substitutions of amino acids in related proteins. These matrices are used to bring out the similarities between various sequences. Users can use PAM, BLOSUM or customized matrices. These can be found or stored in Vector NTI Matrices folder.
It has a simple interface. Users must load a matrix from the matrices folder for them to be able to modify or review a matrix. It contains two tabs: Score matrix and Stats-Table. The Score Matrix tab provides the matrix residues’ name and order. The matrix values can be modified and can be saved in a new output file. The Stat-Table tab provides information about the Lambda and Kappa parameters. These parameters are used to calculate the statistical significance of segments or subligaments. Users can also alter the matrix value and save them in a new output file.