Bioinformatics toolbox - featuresmap question

Hi,

I'm trying to plot the annotations corresponding to a chromosome, and I would like to plot only a small region of the chromosome. I can use something like this:

 chrI_gbk = getgenbank('NC_001133');
 featuresmap(chrI_gbk, {'CDS'});

but this plots all the genes on a vertical axis. Is it possible to plot only a region, say base pairs 1:5000, and display the genes on a horizontal axis?

Thanks!

Razvan

Answer 1

[Lucio Cetto]

Razvan:

featuresmap cannot do what you need, you'll need to plot the CDS manually, hopefully this gets you started:

figure
hold on
chrI_gbk = getgenbank('NC_001133');
cds = featuresparse(chrI_gbk,'Feature','CDS')
yo = 5;
for i = 1:numel(cds)
  starts = cds(i).Indices(1:2:end);
  stops = cds(i).Indices(2:2:end);
  plot([min(starts),max(stops)],[yo yo]/2,'b')
  for j = 1:numel(starts)
     px = [starts([j j]) stops([j j])]; % x-coordinates for patch
     py = [0 yo yo 0];            % y-coordinates for patch
     hq = patch(px,py,'b','FaceColor',[0.8 0.8 1],'EdgeColor','b','Tag','cds'); 
  end
end
fixGenomicPositionLabels
axis([1 50000 -1 30])

HTH Lucio

[Razvan]

Thank you very much!