Learn more about Bioinformatics Toolbox

seqdotplot - Create dot plot of two sequences

Syntax

seqdotplot(Seq1, Seq2)
seqdotplot(Seq1,Seq2, Window, Number)
Matches = seqdotplot(...)
[Matches, Matrix] = seqdotplot(...)

Arguments

Seq1, Seq2	Nucleotide or amino acid sequences. Enter two character strings. Do not enter a vector of integers. You can also enter a structure with the field Sequence.
Window	Enter an integer for the size of a window.
Number	Enter an integer for the number of characters within the window that match.

Description

seqdotplot(Seq1, Seq2) plots a figure that visualizes the match between two sequences.

seqdotplot(Seq1,Seq2, Window, Number) plots sequence matches when there are at least Number matches in a window of size Window.

When plotting nucleotide sequences, start with a Window of 11 and Number of 7.

Matches = seqdotplot(...) returns the number of dots in the dot plot matrix.

[Matches, Matrix] = seqdotplot(...) returns the dot plot as a sparse matrix.

Examples

This example shows the similarities between the prion protein (PrP) nucleotide sequences of two ruminants, the moufflon and the golden takin.

moufflon = getgenbank('AB060288','Sequence',true);
takin = getgenbank('AB060290','Sequence',true);
seqdotplot(moufflon,takin,11,7)

Note   For the correct interpretation of a dot plot, your monitor's display resolution must be able to contain the sequence lengths. If the resolution is not adequate, seqdotplot resizes the image and returns a warning.

Matches = seqdotplot(moufflon,takin,11,7)
Matches =
        5552

[Matches, Matrix] = seqdotplot(moufflon,takin,11,7)

See Also

Bioinformatics Toolbox functions: nwalign, swalign

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