The open source software MUMmer is used for sequence alignment of long genome sequences. I do not really understand its name (maybe due to my poor knowledge in biology).
It is MUM (Maximal Unique Matcher):
1. Match: exact match of a minimum length.
Does it mean that it finds the regions of the two sequences that match (that means they are equal) but that have a certain minimum length ?
2. Maximal: cannot be extended in either direction without a mismatch
What does it mean ? By direction we mean the orientation of the DNA strand 5' -> 3' ? But if so, why the match is no more valid for the strand 3' -> 5' ?
3.Unique: occurs only once in both sequences (MUM)
What does it mean ? Or, on the other side, how can it occur only once in a single sequence (MEM) ?
Thank you in advance.
You will find original MUMMER papers linked on this page. It would likely help to read through those. Start with the original MUMmer paper from 1999.
Thank you GenoMax ! At least the third point is more clear with the article thanks to the extract that tells:
However, I still can't understand very well the reason of the term Maximal .
Direction is not critical since DNA is anti-parallel. Maximal is simply saying that the match can't be extended beyond the MUM without causing a mismatch.
Thank you very much !