how to draw an ideogram graph for a chromosome?
Sophia Liu
Wednesday, 26 August 2009 17:27 UTC
Hi, All,
Is there anybody who knows how to draw an ideogram for a chromosome? what’s more, I want to add a mark, such as a triangle, next to certain position.
it’s a little like the ideogram shown in Figure 2 in this paper : “Digital karyotyping”.
Thanks in advance.
Sophia
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Replies
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Nobody in this bioinformatics group knows about this?
:)
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Sophia, you wrote: “it’s a little like the ideogram shown in Figure 2 in this paper : “Digital karyotyping”.”, and complained that nobody answered. However you don’t say which paper. Perhaps you tried to upload an image but it didn’t make it. If I were you I’d repost with a link.
David
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Sophia, you wrote: “it’s a little like the ideogram shown in Figure 2 in this paper : “Digital karyotyping”.”, and complained that nobody answered. However you don’t say which paper. Perhaps you tried to upload an image but it didn’t make it. If I were you I’d repost with a link.
David
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Hej Sophia, are you referring to this figure/paper: http://www.pnas.org/content/99/25/16156/F2.large.jpg ?
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Hi, Helge, David
Yes, it is the Figure I mean, which is from paper “Digital karyotype”. in this figure, each chromosome is represented by 3 parts, I just want one of those 3 parts: the bottom part , i.e. the ideogram part (with bands colored black).
Do you have any idea?
Thanks
Na -
http://www.biologia.uniba.it/rmc/0-internal-images/z-ideograms/ideograms
http://umanitoba.ca/afs/plant_science/courses/PLNT3140/l18/Idiogram_panel3.jpg
HTH
Paulo
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Hi, Paulo,
I can not read the content in the first link you gave.
For the second link, it only shows the idiograms. For me, what I want to know is how to draw those idiograms.
Do you have any idea about it?
thanks
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There are many ways to draw the ideograms. One of them is to get a list of the cytobands and create some code that will read the start/end positions and then create the structure. Your mileage may vary, of course.
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Hi Sophia,
If I am understanding correctly, ideograms are essentially digital karyotype images.
The first thing you might need is some basic familiarity with a programming language that is capable of drawing graphics. I prefer java and its StdDraw library. However this is purely up to you.
You will need the bp lengths of all the chromosomes (I assume any markers you want to identify will have a bp position tag according to the ref sequence from the human genome sequencing consortium), and for extra credit, you may want to include the start, middle and endpoints of the centromeres (this will just make your chromosomes look more realistic). If you plot the chromosomes on a cartesian plane according to their bp length, you can easily plot any marker as long as you know the marker’s bp location.
This data can all be obtained from http://genome.ucsc.edu/cgi-bin/hgGateway , the USCS genome browser. Unfortunately, other than moving to the start/end of each chromosome, I know no good way of mining the start and end points.
By using the number of bp from the reference sequence as the relative lengths of the chromosome, whenever you plot a position (whether it be a band, triangle, etc.) on the chromosome, it will appear at the proper location.
While I didn’t go into too much detail, I hope this at least points you in the right direction. Let me know if you would like more specific instructions.
Alex
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