Dotplots are one of the earliest pairwise alignments tools used in Molecular Biology. For finding repeats in a sequence, or for finding areas of similarity between two sequences, they are invaluable. The MacVector implementation of DNA matrix analysis uses techniques developed by Pustell. The method enables you to:
- look for regions of similarity between two sequences using a dot matrix plot
- display matching regions as either diagonal lines or as diagonally arranged characters whose values indicate the degree of similarity.
- look for regions of similarity at the amino acid level between a nucleic acid sequence and a protein sequence using a dot matrix plot
- Look for repeats and inverted repeats
This tool allows you to compare two nucleic acid sequences. To use this functionality, at least two nucleic acid sequences must be open, a window containing a nucleic acid sequence must be the active window, and a nucleic acid scoring matrix file must be open or available to the program. The output is a two-dimensional plot, with the residues of one sequence along the X-axis, and the residues of the comparison sequence along the Y-axis.
This allows you to compare two protein sequences. To run this analysis, at least two protein sequences must be open, a window containing a protein sequence must be the active window, and a protein scoring matrix file must be open or available to the program. The output is a two-dimensional plot, with the residues of one sequence along the X-axis, and the residues of the comparison sequence along the Y-axis.
This allows you to compare a nucleic acid and a protein sequence. To run this analysis, at least one protein sequence and one nucleic acid sequence must be open, either sequence may be active and a protein scoring matrix file must be open or available to the program. The output is a two-dimensional plot, with the residues of one sequence along the X-axis, and the residues of the comparison sequence along the Y-axis.
When performing this analysis, MacVector first translates the nucleic acid sequence in the three reading frames of one of the DNA strands (if the strand options of ++ or +- are chosen) or in all six reading frames (if both strands are chosen). The comparison is then performed on the resulting amino acid sequences. The output is a two-dimensional plot, with the residues of the protein sequence along the X-axis, and the residues of the translated DNA sequence along the Y-axis. The aligned sequence display shows each aligned sequence from all the reading frames.