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Journal Article

Large Scale Hierarchical Clustering of Protein Sequences


Krause,  Antje
Max Planck Society;


Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Krause, A., Stoye, J., & Vingron, M. (2005). Large Scale Hierarchical Clustering of Protein Sequences. BMC Bioinformatics, 6, 15-15. doi:10.1186/1471-2105-6-15.

Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-870E-A
Background Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication of currently available search routines it is still virtually impossible to identify quickly and clearly a group of sequences that a given query sequence belongs to. Results We report on our developments in grouping all known protein sequences hierarchically into superfamily and family clusters. Our graph-based algorithms take into account the topology of the sequence space induced by the data itself to construct a biologically meaningful partitioning. We have applied our clustering procedures to a non-redundant set of about 1,000,000 sequences resulting in a hierarchical clustering which is being made available for querying and browsing at http://systers.molgen.mpg.de/. Conclusions Comparisons with other widely used clustering methods on various data sets show the abilities and strengths of our clustering methods in producing a biologically meaningful grouping of protein sequences.