how to draw a very large diagram?
Sophia Liu
Saturday, 19 January 2008 23:24 UTC
Hell, everyone,
I want to map all the transposable elements to each chromosome. However, each chromosome is very long. If I use the matlab to do it, it can’t draw such a large diagram.. Does anyone here know how to accomplish this work?
Anyway, welcome your suggestion.
Best
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Replies
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Hello Na Liu,
You may load your transposable element location data to the UCSC Genome Browser (http://genome.ucsc.edu/, and also see here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks), or alternatively use the free Affymetrix IGB genome broswer to view your data and move alnog the genome interactively (http://www.affymetrix.com/support/developer/tools/download_igb.affx).
To create static pictures programmatically, I recommend to search the R BioConductor library (http://www.bioconductor.org/) for relevant functions.
Additional possibly useful links may be found here: http://bioinfo.bgu.ac.il/bsu/links/index.htm
I hope this helps. Vered -
Have a look at http://www.ncrna.org/idiographica/
Idiographica is a web server that let you create your own idiogram.Pierre
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To do it for X:Map, I wrote a custom Java Swing Layout, so I can show a section of chromosome, then slide the visible window to the right, adding new elements if required for this new window position
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Perhaps gff2ps will do the trick for you if you want to run things locally.
You can also draw graphics in PNG, GIF, or SVG in Perl with Bio::Graphics
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Hello, every friend,
Thanks for your sincere help, which benefited me a lot. Thanks !!!!!!!!!
However, currently, I only know all the Drosophila transpposons within euchromatin region. How could I know the positions of the Drosophila transposons locating in heterochromatin region????? This troubles me greatly.
Welcome your ideas and look forward to your reply.
Best
Na -
As to the graph drawing tools, besides the tools recommended above, you may also want to try argo at http://broad.mit.edu/annotation/argo . You can save your annotations of multiple transposons in some specific formats (GFF3), and then draw the graph using argo. This is a local runnable java program.
As to the transposon mapping, you may use RepeatMasker or just blast to map the known transposons onto the chromosomes. And you can also use some de novo programs to identify repetitive elements. For example, RepeatScout.
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