Genome synteny plotter

rahularjun86 · 09-10-2012, 11:39 AM

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

SES · 09-10-2012, 01:19 PM

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.

jimmybee · 09-10-2012, 04:35 PM

M-GCAT is another (http://alggen.lsi.upc.es/recerca/align/mgcat/)

mbayer · 09-17-2012, 01:51 AM

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

A_Morozov · 09-19-2012, 07:22 PM

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.

lindylou · 09-20-2012, 04:57 AM

Looks like the sanger tool ACT http://www.sanger.ac.uk/resources/software/act/

rahularjun86 · 09-20-2012, 07:37 AM

Hi all,
Many thanks for your valuable comments.

Regards,
Rahul

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09-10-2012, 11:39 AM	#1
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	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 __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany

09-20-2012, 07:37 AM	#7
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	Hi all, Many thanks for your valuable comments. Regards, Rahul __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany

09-10-2012, 01:19 PM	#2
SES Senior Member Location: Vancouver, BC Join Date: Mar 2010 Posts: 275	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.

09-10-2012, 04:35 PM	#3
jimmybee Senior Member Location: Adelaide, Australia Join Date: Sep 2010 Posts: 119	M-GCAT is another (http://alggen.lsi.upc.es/recerca/align/mgcat/)

09-17-2012, 01:51 AM	#4
mbayer Member Location: Dundee, Scotland Join Date: Mar 2009 Posts: 29	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

09-19-2012, 07:22 PM	#5
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	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.

09-20-2012, 04:57 AM	#6
lindylou Junior Member Location: united kingdom Join Date: Oct 2008 Posts: 4	Looks like the sanger tool ACT http://www.sanger.ac.uk/resources/software/act/