seqdotplot matlab,Create dot plot of two sequences

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 a character vector or string for each sequence. 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)

Introduced before R2006a