Hi mauve users,
I used progressivemauve to compare two genomes each saved in the fasta file
format. In each genome file there are more than one sequence corresponding to
the chromosomes. I read in the manual that fasta file containing multiple
sequences will be merged together.
I have two questions:
1) Where do I find the LCBs? Running progressive generated 3 files (.xmfa,
.bbcols, and .backbone). From reading the manual and this forum I had a feeling
that the LCBs are located in the backbone file. However the backbone file has a
lot of records while when I visualize the alignment from the mauve interface it
says there are only few thousands LCBs, a number way low compared to the
records in the backbone file. Could someone please clarify this?
2) Since my interest is on finding the LCBs, how do I go back to find out where
these LCBs are located in the genome after the chromosome sequences have been
merged together? Currently the coordinates seen on the backbone file are
irrespective of the chromosome sequence.
I appreciate your time in clarifying these for me.
Thanks,
Saleh
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