Mauve LCB Meaning
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6.9 years ago
novice ★ 1.1k

I'm having trouble understanding what Mauve's LCB parameter really is. The manual defines it as " the minimum number of matching nucleotides identified in a collinear region for that region to be considered true homology versus random similarity. " I don't even understand what the seed weight really is.

What if I wanted to allow only .02 alignment error, how can I do that? I just don't see how it can be reliable to align with the default LCB then play with the slider until no more "spurious" rearrangements appear.

I would appreciate your clarification. Thank you.

mauve Assembly alignment • 3.1k views
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