n 1970, A.J. Gibbs and G.A. McIntyre (1970) described a new method for comparing two amino acid and nucleotide sequences in which a graph was drawn with one sequence written across the page and the other down the left-hand side.
Whenever the same letter appeared in both sequences, a dot was placed at the intersection of the corresponding sequence positions on the graph
The resulting graph was then scanned for a series of dots that formed a diagonal, which revealed similarity, or a string of the same characters, between the sequences. Long sequences can also be compared in this manner on a single page by using smaller dots.
The dot matrix method quite readily reveals the presence of insertions or deletions between sequences because they shift the diagonal horizontally or vertically by the amount of change. Comparing a single sequence to itself can reveal the presence of a repeat of the same sequence in the same (direct repeat) or reverse (inverted repeat or palindrome) orientation. This method of self-comparison can reveal several features, such as similarity
between chromosomes, tandem genes, repeated domains in a protein sequence, regions of low sequence complexity where the same characters are often repeated, or self-complementary sequences in RNA that can potentially base-pair to give a double-stranded structure. Because diagonals may not always be apparent on the graph due to weak similarity,
Gibbs and McIntyre counted all possible diagonals and these counts were compared to those of random sequences to identify the most significant alignments.
Whenever the same letter appeared in both sequences, a dot was placed at the intersection of the corresponding sequence positions on the graph
The resulting graph was then scanned for a series of dots that formed a diagonal, which revealed similarity, or a string of the same characters, between the sequences. Long sequences can also be compared in this manner on a single page by using smaller dots.
The dot matrix method quite readily reveals the presence of insertions or deletions between sequences because they shift the diagonal horizontally or vertically by the amount of change. Comparing a single sequence to itself can reveal the presence of a repeat of the same sequence in the same (direct repeat) or reverse (inverted repeat or palindrome) orientation. This method of self-comparison can reveal several features, such as similarity
between chromosomes, tandem genes, repeated domains in a protein sequence, regions of low sequence complexity where the same characters are often repeated, or self-complementary sequences in RNA that can potentially base-pair to give a double-stranded structure. Because diagonals may not always be apparent on the graph due to weak similarity,
Gibbs and McIntyre counted all possible diagonals and these counts were compared to those of random sequences to identify the most significant alignments.
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