MATLAB Bioinformatics Tools. Rob Henson The MathWorks, Inc. Who Am I?. Development manager for Bioinformatics group at The MathWorks Natick, MA Software developer Background in algorithm design and software engineering. What do I do?. Write software for bioinformatics Sequence analysis
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>> map = eye(128);
Why does this work?
How could we make this better?
function matches = dotplot(seq1,seq2,window,stringency)
% DOTPLOT Visualize sequence matches.
% DOTPLOT(S,T) plots the sequence matches of sequences S and T.
% DOTPLOT(S,T,WINDOW,NUM) plots sequence matches when there
% are at least NUM matches in a window of size WINDOW. For nucleotide
% sequences a WINDOW of 11 and NUM of 7 is recommended in the
% MATCHES = DOTPLOT(...) returns the number of dots in the dotplot
% moufflon = getgenbank('AB060288','sequence',true);
% takin = getgenbank('AB060290','sequence',true);
% This shows the similarities between prion protein (PrP) nucleotide
% sequences of two ruminants, the moufflon and the golden takin.
% See also NWALIGN, SWALIGN.
seq = ‘MATLAPEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSP’;
seqmw = mw(seq-’A’+1);
1. Create a hydrophobicity plot
You can get the amino acid values from http://cn.expasy.org/cgi-bin/protscale.pl
Use Kyte & Doolittle’s values.
Create a function that has two inputs, the sequence and the window size. The function will create a hydrophobicity plot. The help for the function is on the next slide…
% HYDROPHOBIC plots the hydrophobicity of an amino acid sequence
% HYDROPHOBIC(SEQUENCE,WINDOW_LENGTH) creates a hydrophobicity plot of
% SEQUENCE using a smoothing window of length, WINDOW_LENGTH.
% SEQUENCE must be a valid amino acid sequence. If SEQUENCE contain any
% symbols other than the standard 20 amino acid letters, the function
% will give an error message. SEQUENCE can be either upper or lower case.
% WINDOW_LENGTH must be an odd positive integer.
2. Modify the function to return the maximum and minimum hydrophobicity values in the plot.
Make appropriate changes to the help for the function.