A Customized force-directed layout algorithm for biological graphs whose vertices have enzyme commission attributes

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2015

Author

Danacı, Hasan Fehmi

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Force directed layout algorithm is popularly used to draw biological graphs. However, it employs only graph structure. When we would like to embed domain-specific knowledge, such as biological or chemical attributes related to the vertices, force directed layout algorithm should be modified. It is then important to draw more readable layouts for biologists without the dispose of aesthetically pleasing way that comes from force-directed algorithm’s nature. This thesis aims to describe a modified and improved force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the vertices are identified with EC (Enzyme Commission) numbers. The vertices with the same EC class numbers are treated as members of the same cluster. Positions of vertices in clusters are affected by mainly two factors: biological similarity of each vertex in the same cluster and theoretical length between the vertices. EClerize is tested on a number of biological pathways and the improvement with respect to the original algorithm is presented.

Subject Keywords

Graph algorithms., Computer algorithms., Information visualization., Enzymes

URI

http://etd.lib.metu.edu.tr/upload/12619592/index.pdf
https://hdl.handle.net/11511/25330

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Graduate School of Natural and Applied Sciences, Thesis

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Citation Formats

H. F. Danacı, “A Customized force-directed layout algorithm for biological graphs whose vertices have enzyme commission attributes,” M.S. - Master of Science, Middle East Technical University, 2015.