Create dot plot of two sequences
seqdotplot(Seq1,Seq2, Window, Number)
Matches = seqdotplot(...)
[Matches, Matrix] = seqdotplot(...)
|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.|
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.
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)