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

[Aaron D. <aar...@ut...>]

Hi Karla,
The "1. no extension" file you mention is the XMFA file.
Now, onto your question about LCB boundaries, the quantities you are
asking for actually ill-defined. The issue is that when unequal gene
content is present in a genome alignment, and there are three or more
genomes involved, it is no longer possible to precisely delimit the
boundaries of LCBs. The blocks reported by progressiveMauve can have
(but do not always have) arbitrary endpoints that do not necessarily
indicate exactly where the rearrangement breakpoint is located.
Nevertheless, if you want to simply convert the coordinates in the
XMFA, which use a coordinate system defined by concatenating all
contigs in a genome in the order they appear in the input file, to
contig-local coordinates that should be possible, and would require you
to do a bit of custom scripting.
Best,
-Aaron
On Fri, 2016-10-07 at 12:13 -0300, Karla Pollyanna wrote:
> 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, 
> 
> 
> 
>  Sent with Mailtrack
> 
>   		 Karla Pollyanna Vieira de Oliveira
> Biologist / MSc. Bioinformatics, Laboratório de Tecnologias
> Integradas (InteLab)  +55 48 9133-9078 | +55 31 987-677-667 | karla.b
> iot...@gm... | ka...@in... | Skype:
> karla_pollyanna   
> 
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-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman





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