[BioPython] How can I draw genome comparison figure to publish?

[Leighton Pritchard]

Hi Kyoung-Ho,

On 17/03/2009 12:02, "mgenome" <mgenome at gmail.com> wrote:

> Two genomes should be compared by their ORFs similarities calculated by
> BLASTP or stretcher etc.
> 
> If there is a table like this
> 
> ORF1, start, stop, strand, ORF2, start, stop, strand, similarity,
> genome1_ORF1, 1, 200, +, genome2_ORF1, 1,  300,  -, 50
> genome1_ORF2, 201, 400, +, genome2_ORF3,  320, 500, -, 90
> ....
> 
> the programs or library should draw as follows;
> ===>   ===> ....
>  |          |
>  |          |
>  |          |
> <===  <===  ....
> Their different similarities should be represented by different colors of
> linker lines.
> 
> I examined several programs, but I didn't find the program good enough to
> use for publication.
> ACT (Artemics) can draw comparison figure but it can not show ORFs well.
> inGeno is the program close to what I want. But It cannot compare multiple
> genomes and I want to draw ORF as arrows. I know GenomeDaigrams in python do
> not support comparison of ORFs in genomic level.

GenomeDiagram does not draw the linker lines you require, I'm afraid.  The
package I would use to do so is ACT, and I have published diagrams created
using ACT (figure 3 in http://dx.doi.org/10.1073/pnas.0402424101).  There is
also M-GCAT (http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html),
which is very similar to ACT, and perhaps so similar that it will have the
same problems when generating publication-quality images to your liking.
GCV (http://zamov.online.fr/projects/gct/) I've never tried.
 
> Does anybody know a program and library to draw genome comparion figure
> showing ORF comparison.  I known that it is stupid to want a perfect program
> to fulfill all my requirments, but I want to find program or library to
> fulfill a part of my requirements.

GenomeDiagram does not currently have a facility to indicate synteny in the
way that you require using linker lines, so it may not be the tool you need
just yet.  However, it has been used to indicate the results of comparisons
between ORFs on the whole-genome level, using the colours of the compared
features to indicate the sequence identities of the matches (e.g. Figure 2
in http://dx.doi.org/10.1146/annurev.phyto.44.070505.143444 and
http://apsjournals.apsnet.org/doi/abs/10.1094).

Cheers,

L.


-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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