[Mauve-users] Extracting coordinates of LCB

[Cedric C. <ced...@sf...>]

Hello

The Mauve file formats guide (http://darlinglab.org/mauve/user-guide/files.html) states that one can obtain a permutation matrix file, together with an LCB boundary file. I am using the version 2.4 of Mauve, through the GUI, to align a few bacterial genomes, but when I export, through the GUI, the permutation I do not obtain the LCB boundary file. 

Is-it a feature that is not available any more in Mauve 2.4, or that can be obtained through the command line ?

To be complete, I tried to obtain LCB boundaries from the backbone file, but the permutation exported through the GUI has 72 blocks, and the permutation I obtain from the backbone has 58 colinear blocks, and the rearrangement history I obtain from both are very different so I assume I missed something in interpreting the backbone file properly.

So I'd be happy to know how to obtain the LCB boundary coordinates.

Thanks

Cedric Chauve, PhD
Professor, Department of Mathematics
Simon Fraser University
http://paleogenomics.irmacs.sfu.ca/
http://www.cecm.sfu.ca/~cchauve