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Vertical Hamming Distance (VHD) is a tools to compute hamming distance between two string at \textit{bare metal} "\textit{bare metal}"  speed. Essantialy, it means VHD do comparison between two string at or near speed of system's processor. Moreover, VHD has an embedded edit-distance base filter which can quickly determine whether the minimum number of edits (the tools only support substitution not insertion and deletion) is smaller than a user defined threshold \textbf{T}. We also improved VHD's filtering power by considering coding scheme of our alphabet in data genomic databses.