How To Draw Plasmid Map

Question

[HG]

Hi everyone i need to draw such a plasmid map i mention bellow. Can anyone help me out. Its published in

http://jac.oxfordjournals.org/content/early/2013/11/19/jac.dkt464.long In this paper.

Thanks advance.

Answer 1

[Peter]

This requires programming in Python, but you can make something similar in Biopython using GenomeDiagram with cross-links, see e.g. http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/

The Biopython Tutorial covers an example leading up to a variant of Proux et al (2002) Figure 6, with the sample code here: https://github.com/biopython/biopython/blob/master/Doc/examples/Proux_et_al_2002_Figure_6.py

A more complicated example made in the same way appears in http://dx.plos.org/10.1371/journal.pone.0040683 as Figure 2:

[HG]

Thanks for the reply. But could you please let me know : my problem like that: I have two plasmid from different bacterial species and now i assembled and made final pseudogenome. Now i want to compare two plasmid in such a way that i can show both the plasmid have similar kind of resistance cassette. Could you please suggest me what i will do next and what will be input for biopython .Because i am new in this field. Please help me out.

[Peter]

You need to decide what to draw as the genomes (e.g. two tracks for the two plasmids) and which regions have enough similarity to cross link on the figure (e.g. using BLAST matches). Once you've planned that, to use this code you will need to learn to program in Python (there is no easy to use GUI for this Biopython/GenomeDiagram based approach).