Tag Archives: graph

Graphs

graph
Clustering Coefficient
clusting coefficient

The clustering coefficient for graph is just the average of the clustering coefficients of the nodes in the graph.
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Networks

Chain networks consist of a set of nodes and a sequence of edges between them connect them into a single chain.

chain ={}
for i in range(n-1):
    make_link(chain, i, i+1)
0——–0——–0——–0——–0
n1 e1 n2 e2 n3 e3 n4 e4 n5   – nodes (n), edges (e) = n-1
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Graph, Eulerian Path, Eulerian Tour

Algorithms areGraph just how we organize computations to solve a particular problem. Some algorithms are really straightforward, but other algorithms take advantage of subtle mathematical properties to quickly and accurately provide an answer.

A set of circles and lines connecting between them is graph.
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Graph – Overlap, De Bruijn

1. String Composition: Form the k-mer composition of a string.
Input: An integer k and a string Text.
Output: Compositionk(Text), where the k-mers are written in lexicographic order.
Composition3(TATGGGGTGC) = ATG, GGG, GGG, GGT, GTG, TAT, TGC, TGG

dnas = [in_dna[i:i+k] for i in range(0, len(in_dna)) if len(in_dna[i:i+k])==k]
dnas.sort()

For example TAATGCCATGGGATGTT are linked together to form the genome path.

s1
For example, each of the three occurrences of ATG should be connected to TGC, TGG, and TGT; these connections are overlapping 3-mers. The graph showing all overlap connections.

s2
The structure in the figure above is an example of a graph, or a network of nodes connected by edges. This graph is an example of a directed graph, whose edges have a direction and are represented by arrows (as opposed to undirected graphs whose edges do not have directions).

Sequence much shorter DNA fragments called reads.

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