Re: [Mauve-users] Mauve statistics

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

Hello Mathias,
The information you are asking for exists in the XMFA file, and in fact
if you just delete the sequences from the XMFA file the representation
of that information becomes fairly succinct. Maybe a clever series of
grep commands could get you there, or some regular expressions.
I guess you are seeking this information in a tab delemited format?
There are no programs bundled with Mauve that would produce the info in
a such a format. The closest would probably be the .bbcols and
.backbone files, but those also break up the blocks at the boundaries
of gain & loss events that are longer than around 20nt, so probably
wouldn't be quite what you want for your score idea. Not sure if its
helpful for your goals, but Mauve has a few rearrangment distances
implemented in the GUI, including double-cut join and single-cut join,
and breakpoint counts themselves have been used as a statistic for
genome rearrangement. These distances can only be defined on genome
alignments that have equal gene content in all genomes, which isn't
usually the case with progressiveMauve unless the subset LCBs have been
stripped out, or just 2 genomes were aligned.
Best,
-Aaron
On Wed, 2017-02-08 at 06:51 -0500, Mathias Lorieux (GMail box) wrote:
> Hi all,
> 
> I’d be grateful if I could get help on how to obtain summary
> statistics on alignments that Mauve produces. 
> 
> What I am looking for is a summary of the rank position, size, start-
> stop of each ’block’ that Mauve identifies, for each compared
> sequence. 
> 
> From these statistics I aim to calculate a kind of re-shuffling score
> between two sequences.
> 
> Thanks very much,
> Mathias
> 
> 
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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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