Genome synteny plotter

[rahularjun86]

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.

Best wishes,
Rahul

[SES]

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]

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

[mbayer]

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]

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]

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

[rahularjun86]

Hi all,
Many thanks for your valuable comments.
Regards,
Rahul