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.