Graphical representation of gene level synteny between genomic regions

[Hobbe]

So, I have a de novo sequenced genome that has a section deleted when compared to a closely related species. Basically, around the deleted region, synteny is strongly preserved with orthologous genes lining up nicely, but then there is suddenly a region with three genes that is deleted when compared to the well-known and closely related species. This is of big biological relevance and I want to make a graphical representation of this to use in a publication.

I really like the look of Sybil, but installing this database-dependent program just seems to be an overkill for my fairly limited intended use. This picture shows pretty much what it is I want to do, although I will probably limit myself to two genomes: http://sybil.sourceforge.net/screens...in_cluster.png

Is there a easy-to-use tool I could use for this purpose? Note that I want the genes depicted in there, with orthology shown using connecting lines. ACT or Mauve are not options as I understand it as they do not include genes in their output.

Cheers,
Henrik

[rhinoceros]

ACT or Mauve are not options as I understand it as they do not include genes in their output.

Cheers,
Henrik

As far as I know, as long as you include annotation data (e.g. use .gbk files), mauve includes genes in output. I could be wrong..

[Hobbe]

As far as I know, as long as you include annotation data (e.g. use .gbk files), mauve includes genes in output. I could be wrong..

No, you are right. That was my mistake. However, I can't say I really like the output of that one, so I'd really like to get more suggestions that give more clear "easy on the eye" output.

[SES]

I think it will be hard to find a tool that is capable of plotting synteny for features between multiple genomes that does not use a database and/or browser. Part of this is computational efficiency so you have a persistent store of features, and don't have to load and parse large files every time you make a qurey. I have been most pleased with the results from GBrowse_syn, but the usage and installation is not simple. For a small region, you may want to consider using ggbio with R/bioconductor. You may be limited with the type of results you can generate, though.

This is a problem I had in the past, where I found that some programs are easy to use (like Mauve) but the display is too busy or not to my needs, and other programs are a lot more involved but they give you more flexibility with what you generate. It is really a matter of how much time you want to invest in this project.

[mbayer]

Hi Henrik,

try Strudel (http://bioinf.hutton.ac.uk/strudel/) -- this may be just what you are after.

I was the main developer on Strudel while it was actively being developed, but we now don't really have support for it any more. It might still be useful for you in its current incarnation though.

Strudel just takes flat files as input - it has its own data format, but it's basically just a tab delimited text file you can rattle up in Excel quickly.

cheers

Micha