Hi,
I'm looking at the backbone file from a progressive mauve alignment in an excel
spreadsheet, doing a bit of a "sanity check" on my data. I've noticed that
there
are some aligned regions which seem bizarrely short, as short as 2 bp, it seems
like these should have been removed by the step of the algorithm which removes
insignificant matches? I was going to just chuck them out, but i figured i
should check it didn't indicate something had gone wrong first? (I used the
default settings plus iterative refinement, 2 of my genomes were drafts with
~200 contigs.)
Also, do the negative numbers in the backbone file just mean the co-ordinates
are on the reverse strand? I can't think of anything else they could mean, but
i
can't find anywhere that states this explicitly.
thanks from,
kirstin
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