Markus Schmidt

Research Student


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Mr. Schmidt started working as research student in spring 2015. His research interests are within the topics of cluster analysis and computational gene analysis.

 

He is currently working on:

  • Development of an application for gene analysis and gene prediction on the foundation of C++11.
  • Development of an application / algorithm for cluster analysis of biological data.

A novel specialized single linkage clustering algorithm for taxonomy analyses

Mr. Schmidt, Prof. Kutzner and Prof. Heese developed a novel algorithm for taxonomy analyses. Mr. Schmidt implemented the novel algorithm as well as a plain single linkage approach.

Source files as well as the executable jar file of the reference implementation can be obtained here.
The application does not perform alignment, it merely loads Klee-diagrams. Some example diagrams can be downloaded here. The files are given in Excel-xml format, so it is possible to inspect the raw data using Microsoft Excel.

The algorithm is intended to enable big-data analyses of orthologue genes, by breaking the time complexity of general single linkage clustering. This is achieved using the taxonomic order of species.

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