how to visulize gene synteny alignment

[cascoamarillo]

Just to keep it updated. I found one program really usuful:
Easyfig http://sourceforge.net/projects/easyfig/

Still, annotations come in genbank file, but you are able to load a custom graph file. So it is easy to plot the synteny along the coverage plot for each sequence if you include a file with one column of plot values (they can be extracted from bam->bedgraph).
Apparently, it would read .ace file for coverage graph; though I have no Idea how to convert sam/bam into ace.

[maubp]

You can include heat maps and line graphs in Biopython's GenomeDiagram, although this isn't covered in the Tutorial currently ( http://biopython.org/DIST/docs/tutorial/Tutorial.html and http://biopython.org/DIST/docs/tutorial/Tutorial.pdf ), which focused on genomic feature tracks. Have a look at https://github.com/biopython/biopyth...nomeDiagram.py and its output for a flavour, but this is going to be a bit harder.

[cascoamarillo]

Hi,
I come across a synteny analysis, and I've been trying all this different software solutions along with the ones mentioned in this other post

http://seqanswers.com/forums/showthread.php?t=32803

So mauve and artemis/act can do the trick easily (though you have to deal with genbank files if you'd like to represent features). Genome Diagram module from biopython is quite useful too. I like more working with gff files instead, but right now I don't have too much time for installing and make GMOD GBrowse Syn work.

Is there any new tool I haven't heard yet? For instance, I would like to represent coverage from bam files in the same plot along the synteny; could it be possible to implement that on biopython? I Know artemis can visualize bam files, but not act which is the one showing the comparison file. Any input would be appreciated. Thanks

[NGS group]

This is not a point-and-click solution, but if you can program in Python I would suggest Biopython's GenomeDiagram module with cross-links between features:

http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/

http://www.slideshare.net/etalevich/biopython-project-update-bosc-2012

http://biopython.org/DIST/docs/tutorial/Tutorial.html

This example http://biopython.org/SRC/biopython/D...02_Figure_6.py produces the following image:
http://biopython.org/DIST/docs/tutor...track_cl2a.png

Hi Peter,

Thank you very much for your reply. That is what I want, and I will try it. I know this is not easy work. Before I tried GenoplotR, which is written by R. However the toturial is not clear for me and also very complicated.

Anyway, thanks a lot for your answer.

ZK

[maubp]

This is not a point-and-click solution, but if you can program in Python I would suggest Biopython's GenomeDiagram module with cross-links between features:

http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/

http://www.slideshare.net/etalevich/biopython-project-update-bosc-2012

http://biopython.org/DIST/docs/tutorial/Tutorial.html

This example http://biopython.org/SRC/biopython/D...02_Figure_6.py produces the following image:

http://biopython.org/DIST/docs/tutorial/images/three_track_cl2a.png

[NGS group]

Hi,

Is there anyone can tell me some easy tools that can visulize/plot gene synteny alignment as the picture attached?

Thank you very much!

ZK