Documentation

This is machine translation

Translated by Microsoft
Mouse over text to see original. Click the button below to return to the English verison of the page.

seqdotplot

Create dot plot of two sequences

Syntax

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

Arguments

Seq1, Seq2Nucleotide 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.
WindowEnter an integer for the size of a window.
NumberEnter 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

|

Introduced before R2006a

Was this topic helpful?