computer science

MUMmer

MUMmer is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand MUMmer rather than just read about it. In short: MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure.

Key takeaways

MUMmer belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect MUMmer to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of MUMmer from memory before moving on to harder problems.

Reference excerpt

MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure. It has been used for comparing different genomes assemblies to one another, which allows scientists to determine how a genome has changed. The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs. The original algorithms in the MUMMER software package were designed by Art Delcher, Simon Kasif and Steven Salzberg. Mummer was the first whole genome comparison system developed in Bioinformatics. It was originally applied to the comparison of two related strains of bacteria. The MUMmer software is open source. The system is maintained primarily by Steven Salzberg and Arthur Delcher at Center for Computational Biology at Johns Hopkins University. MUMmer is a highly cited bioinformatics system in the scientific literature. According to Google Scholar, as of early 2013 the original MUMmer paper (Delcher et al., 1999) has been cited 691 times; the MUMmer 2 paper (Delcher et al., 2002) has been cited 455 times; and the MUMmer 3.0 article (Kurtz et al., 2004) has been cited 903 times.

Overview Mummer is a fast algorithm used for the rapid alignment of entire genomes. The MUMmer algorithm is relatively new and has 4 versions.

Versions of MUMmers

MUMmer1 MUMmer1 or just MUMmer consists of three parts, the first part consists of the creation of suffix trees (to get MUMs), the second part in the longest increasing subsequence or longest common subsequences (to order MUMs), lastly any alignment to close gaps. Interruptions between MUMs-alignment, are known as gaps. Otherther alignment algorithms fill these gaps. The gaps fall in the following four classes:

An SNPinterruption – when comparing two sequences, one character will differ. An insertion – when comparing two sequences, there is a subsequence in only appears in one of the sequences. It would be an empty gap in the other sequence at the moment of comparison of the two sequences. A highly polymorphic region – when comparing two sequences, there can be found a subsequence in which every single character differs. A repeat – it's the repetition of a sequence. Since MUMs can only take unique sequences, that gap can be one repetition of one of the MUMs.

MUMmer 2 This algorithm was redesigned to require less memory and increase speed and accuracy. It also allows for bigger genomes alignment. The improvement was the amount stored in the suffix trees by employing the one created by Kurtz.

MUMmer 3 According to Stefan Kurtz and his teammates, "the most significant technical improvement in MUMmer 3.0, is a complete rewrite of the suffix-tree code, based on the compact suffix- tree representation of" the tree described in the article "Reducing the space requirement of suffix trees".

MUMmer 4 According to Guillaume and his team, there are some extra improvements in the implementation and also innovation with Query parallelism. "MUMmer4 now includes options to save and load the suffix array for a given reference." This allows the suffix tree can be built once and constructed again after running it from the saved suffix tree.

Software - Open Source MUMmer has open-source software and can be accessed online.

Related Sequence Alignments There are other types of sequence alignments:

Edit distance BLAST Bowtie BWA Blat Mauve LASTZ BLAST

References

External links MUMmer home page MUMmer2 Book MUMmer Software MUMmer3 MUMmer1 MUMmer4

Worked examples

Example 1 — a first encounter with MUMmer

Start with the simplest possible case. Write down what MUMmer claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to MUMmer before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about MUMmer ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of MUMmer

In research: MUMmer appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses MUMmer in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: MUMmer is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics software, so understanding it makes those chapters shorter.
In everyday life: Look for MUMmer outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study MUMmer in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what MUMmer means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain MUMmer out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is MUMmer in simple terms?

MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure.

Why does MUMmer matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study MUMmer?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on MUMmer.