I have found the software Mauve very useful in illustrate the alignment among
several genomes. And I plan to extensively use it in my current work. I have a
few questions arising my using of Mauve. Could you please help me with them?
1. As in this picture (in my personal web site), I know that the blocks over
the chromosome line are on positive strand and those under the line are on
negative strand. But I also found some yellow boxes that cross the line. What
are these blocks?
http://csbl.bmb.uga.edu/~ffzhou/mauve/example.jpg
2. After I generated the alignment among several genomes and got the results
(*.mln.*), I can view the alignment in the Mauve viewer and estimate the number
of blocks with different minimum LCB weight.
But how could I get the detailed information (e.g. start and end positions, and
strand) of the blocks with a given minimum LCD weight automatically? So that I
could process them with my perl scripts.
Are there any available programs to do this task?
Thank you!
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