#2 Islands for Progressive Mauve

[Aaron Darling]

Progressive Mauve generates a .backbone file that includes a listing of sequence coordinates for all conserved regions identified by an alignment. Regions that are unique to a single genome are not listed in the .backbone file, and may be considered "islands" unique to a particular genome. Islands are the complement of backbone. It would be nice to have a ".islands" file for progressive Mauve alignments.
Generalizing this idea, it may be nice to identify islands among particular subgroups of the aligned taxa.

[Nobody/Anonymous]

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good

[Nobody/Anonymous]

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I have been working with MAUVE for a couple of months and I have found it very useful on my research, however, I agree for the need of the islands file, and for my research is of extreme priority. At our lab, we have developed a Perl Script for analyzing the variability in subsets of genomes, and we were using as input file the .islands file. We have been trying to adapt the new .backbone for our script, however, since we need the positions in the genome of both genomes that are varying, and with the current backbone file I haven't find the way to do it, without being very labor intensive.

Sincerely,

Alejandro Reyes

[Anna Rissman]

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This is sort of done; Look at Mauve analysis package from 2007_whatever_load_etc branch (main class in org.gel.mauve.analysis.MauveInterfacer); takes an alignment file as input; opens alignment and also outputs files. If this format is ok, we could make a cleaner way of accessing it (but doesn't output from alignment, runs after an alignment is made. Also includes other output. . .

Let me know if you want to use this. . .