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In computational molecular biology, gene regulatory binding sites predictionin whole genome remains a challenge for the researchers. Now a days, the genomewide regulatory binding site prediction tools required either direct patternsequence or weight matrix. Although there are known transcription factorbinding sites databases available for genome wide prediction but no tool isavailable which can construct different weight matrices as per need of user ortools available for large data set scanning by first aligning the inputupstream or promoter sequences and than construct the matrices in differentlevel and file format. Considering this, we developed a DNA MATRIX tool forsearching putative regulatory binding sites in gene upstream sequences. Thistool uses the simple biological rule based heuristic algorithm for weightmatrix construction, which can be transformed into different formats aftermotif alignment and therefore provides the possibility to identify the mostpotential conserved binding sites in the regulated genes. The user mayconstruct and save specific weight or frequency matrices in different form andfile formats based on user based selection of conserved aligned block of shortsequences ranges from 6 to 20 base pairs and prior nucleotide frequency beforeweight scoring.

DNA-MATRIX a tool for DNA motif discovery and weight matrix construction