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Dotplots in MacVector 
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Joined: Thu Dec 07, 2006 6:20 pm
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Location: Cambridge, UK
Post Dotplots in MacVector
Dotplots are one of the earliest pairwise alignments tools used in Molecular Biology. But for finding repeats in a sequence, or for finding areas of similarity between two sequences, they are still invaluable.

The MacVector implementation of matrix analysis uses techniques developed by Pustell. These types of analysis are more commonly refered to as DotPlots. There are three types of alignment possible:

Pustell DNA matrix

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.

- look for regions of similarity between two nucleic acid 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.

Pustell protein matrix

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.

- look for regions of similarity between two protein 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.

The match and mismatch scores used in scoring the comparison can be reassigned, or new scoring matrices can be created and edited.

Pustell protein/DNA matrix


To run this analysis, at least one nucleic acid sequence file and one protein sequence file must be open, and a window containing a sequence must be the active window. A protein scoring matrix file must be open or available on disk.

- look for regions of similarity at the amino acid level between a nucleic acid sequence and a protein sequence using a dot matrix plot
- display matching regions as either diagonal lines or as diagonally arranged characters whose values indicate the degree of similarity.

The match and mismatch scores used in scoring the comparison can be reassigned, or new scoring matrices can be created and edited.

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.

Incidentally the output of these has been enhanced in the soon to be released MacVector 10.5


Thu Oct 23, 2008 10:58 am
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