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Old 09-10-2012, 10:39 AM   #1
rahularjun86
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Default Genome synteny plotter

Hi all,
With four sequenced genomes, I want to generate the publishable graphics for the syntenic regions. I could not find the software used in this article (http://www.nature.com/ng/journal/v44...g.2375_F2.html). I am wondering if there is any free software to do this. Thanks in advance for your suggestions.
ng.2375-F2.jpeg
Best wishes,
Rahul
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Old 09-10-2012, 12:19 PM   #2
SES
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That plot looks like something generated with Mauve, but it may not be. Anyway, you should be able to run progressiveMauve and generate something very similar.
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Old 09-10-2012, 03:35 PM   #3
jimmybee
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M-GCAT is another (http://alggen.lsi.upc.es/recerca/align/mgcat/)
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Old 09-17-2012, 12:51 AM   #4
mbayer
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Hi Rahul,

try Strudel (http://bioinf.scri.ac.uk/strudel/) -- it might do the trick for you, and it looks pretty in a publication. It's perhaps better suited for doing comparisons at the chromosome level, but the data structure is flexible and there is nothing to stop you from packaging your whole genome as if it were a single chromosome. If you have any trouble with it I am happy to help (I was the main developer on this project).

cheers

Micha
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Old 09-19-2012, 06:22 PM   #5
A_Morozov
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Kind of related question. Is there any tool to nicely visualize rearrangement scenario (e.g. reconstructed by MGR(A), COGNAC, GRAPPA, etc)? That is, I have ancestral genomes, sequence of operations on them and extant genomes and want to see how they evolved in series of nice, human-readable pictures.
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Old 09-20-2012, 03:57 AM   #6
lindylou
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Looks like the sanger tool ACT http://www.sanger.ac.uk/resources/software/act/
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Old 09-20-2012, 06:37 AM   #7
rahularjun86
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Hi all,
Many thanks for your valuable comments.
Regards,
Rahul
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