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-   -   graph for relationship of homologous genes (http://seqanswers.com/forums/showthread.php?t=35937)

pony2001mx 11-19-2013 04:53 AM

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!

pony2001mx 11-19-2013 05:08 AM

1 Attachment(s)
Sorry, I failed uploading the images. Please find the image here. THANKS.

maubp 11-19-2013 09:00 AM

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

pony2001mx 11-20-2013 03:45 AM

thank you for your suggestions!


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