How to do genome-genome comparison

garethboy · 09-07-2012, 09:27 PM

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

A_Morozov · 09-19-2012, 07:41 PM

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.

ekg · 10-01-2012, 07:18 AM

Have you looked at mummer?

themerlin · 10-01-2012, 10:01 AM

Maybe brig is what you have in mind?

http://sourceforge.net/projects/brig/

bioinfotlc · 12-20-2012, 02:11 AM

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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09-07-2012, 09:27 PM	#1
garethboy Member Location: Kuala Lumpur Join Date: Feb 2012 Posts: 19	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

09-19-2012, 07:41 PM	#2
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	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.

10-01-2012, 07:18 AM	#3
ekg Member Location: Boston, MA Join Date: Apr 2010 Posts: 36	Have you looked at mummer?

10-01-2012, 10:01 AM	#4
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	Maybe brig is what you have in mind? http://sourceforge.net/projects/brig/

12-20-2012, 02:11 AM	#5
bioinfotlc Junior Member Location: Malaysia Join Date: Dec 2012 Posts: 3	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