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What is the meaning of the name MUMmer ?

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.

mummerplot dna alignment mummer sequence
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written by Student • Student

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.

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written by GenoMax GenoMax

Thank you GenoMax ! At least the third point is more clear with the article thanks to the extract that tells:

An MUM is a subsequence that occurs exactly once in Genome A and once in Genome B, and is not contained in any longer such sequence.

However, I still can't understand very well the reason of the term Maximal .

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written by Student • Student

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.

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written by GenoMax GenoMax

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