[BioPython] How can I draw genome comparison figure to publish?
mgenome
mgenome at gmail.com
Tue Mar 17 12:02:42 UTC 2009
I have the whole genome sequence of a phage to compare it's ORFs to those of
other related phages. I want to draw a comparison figure of two or more
genomes.
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.
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.
Thank you in advance.
Kyoung-Ho Kim, Korea.
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