[Mauve-users] Extract coordinates from LCB blocs without xmfa file

[Karla P. <kar...@gm...>]

Dear all,

I'm struggling in a Mauve analysis and wonder if someone could help me.

I'm studying 13 genomes from diff bacteria and I performed a
progressiveMauve alignment from the graphical interface using the last
version of Mauve snapshot for Linux (2015-02-13).

I have as output the follow files: 1. no extension (I use to open the
graphical interface); 2. .backbone; 3. .bbcols ; 4. .guide_tree.

I would like to have the coordinates from LCBs, since I have multiple
genomes and they have up to 900 scaffolds. As example, I would like to an
output such as:

           scaffold                  start         end        genome strand

*      NZ_KB902575.1    1695199    1695311    -  *

I checked in the list and saw an answer from Aaron about xmfa2maf but,
since I don't have a .xmfa file I tried it but I got a kinda NT file that
does not have every LCB.

Does anyone know how can I get what I'm looking for?

Thank you in advance.

Best,



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*Karla Pollyanna Vieira de Oliveira*
Biologist / MSc. Bioinformatics, Laboratório de Tecnologias Integradas
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