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Old 11-19-2013, 04:53 AM   #1
pony2001mx
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Default graph for relationship of homologous genes

Dear All,
Could you please inform me what softwares can be used to generate the following graphs. Both depict relations of synteny blocks. I only focus on ~100 hundred genes in three genomes. I can perform blast to find these 100 genes' positions, and then need to generate a graph like the following. THANKS A LOT!
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Old 11-19-2013, 05:08 AM   #2
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Sorry, I failed uploading the images. Please find the image here. THANKS.
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File Type: bmp _temp2.bmp (141.8 KB, 23 views)
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Old 11-19-2013, 09:00 AM   #3
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I'm not sure what was used for the example in your image - if it was from a paper posting the reference & DOI might help.

You might want to look at Mauve, or ACT (Artemis Comparison Tool).
http://gel.ahabs.wisc.edu/mauve/
http://www.sanger.ac.uk/resources/software/act/

The fact you want to do ~100 figures does suggest you should look for an automated solution (not just point and click). If you can program in Python, you might consider using Biopython's GenomeDiagram module, see for example:
http://news.open-bio.org/news/2012/0...genomediagram/
http://armchairbiology.blogspot.co.u...n-colours.html
http://www.slideshare.net/etalevich/...date-bosc-2012
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Old 11-20-2013, 03:45 AM   #4
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thank you for your suggestions!
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