A Vertex cover of a graph is a set of vertices such that each edge of the graph is incident to at least one vertex of the set.

I understand the vertex cover problem, but how is it used in bioinformatics?

Application Of "Vertex Cover" In Bioinformatics Problems

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13.1 years ago

Dana
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50

A Vertex cover of a graph is a set of vertices such that each edge of the graph is incident to at least one vertex of the set.

I understand the vertex cover problem, but how is it used in bioinformatics?

8

Entering edit mode

13.1 years ago

Gingi
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330

The vertex cover problem is the basis for *de novo* genome assembly using the overlap-consensus method. Assemblers like CABOG, the Celera assembler, construct an overlap graph of many whole-genome shotgun reads, where each vertex correspond to a read and the edges represent mutual overlap between two reads. The assembler then attempts to find a Hamiltonian path through the graph, where each vertex (read) is visited exactly once. The Hamiltonian path then represents the consensus sequence of the generated assembly.

Despite the effectiveness of the overlap-consensus method for long reads (+800 bp), De Bruijn assemblers have recently become the norm for short-read assembly. These assemblers trace an Eulerian path through a De Bruijn graph, where each edge corresponds to a *kmer* derived from each read and a vertex represents an exact overlap between two kmers.

Read more about genome assembly here. (There is a lot of published literature on this topic, most of it accessible through the links.)

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Maybe a better question would be 'has anyone applied this to a bioinformatics problem?'. There are probably multiple useful applications of this theory to bioinformatics. The question is whether anyone has found them!

I have edited the title of the question.