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Old 09-07-2012, 08:27 PM   #1
garethboy
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Default How to do genome-genome comparison

Besides Artemis, what are the softwares that can perform (1-to-1 or 1-to-many) genome-to-genome(s) comparison? Preferable the results presented in ring form, or with a good visuulization method.

Kindly advise. I am very new in bioinformatics.

Thanks
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Old 09-19-2012, 06:41 PM   #2
A_Morozov
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What exactly kind of comparison do you need? If it's just synteny blocks (ie ones with conserved order across set of genomes), pick MAUVE. If you want to reconstruct some phylogeny using genomic rearrangements, pick MGR or COGNAC, but these require some data preparation. If you want to compare gene content or something like that, write a little Perl or Python script and let it do the work.
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Old 10-01-2012, 06:18 AM   #3
ekg
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Have you looked at mummer?
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Old 10-01-2012, 09:01 AM   #4
themerlin
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Maybe brig is what you have in mind?

http://sourceforge.net/projects/brig/
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Old 12-20-2012, 01:11 AM   #5
bioinfotlc
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Hi, you can try to use SynaCompare (http://synasite.mgrc.com.my/synasuit...enu.jsp?modN=4)
It produce decent 2D dot plot graph for two genomes comparison.
http://synasite.mgrc.com.my/synasuit...user_guide.pdf
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