What is the meaning of the name MUMmer ?
0
1
Entering edit mode
4 months ago
Manuela ▴ 30

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 • 246 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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 .

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you very much !

ADD REPLY

Login before adding your answer.

Traffic: 1170 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6