Large scale hierarchical clustering of protein sequences

Antje Krause, Jens Stoye, Martin Vingron
2005 BMC Bioinformatics  
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. We report on our developments in grouping all known protein sequences hierarchically into superfamily and family clusters. Our graph-based
more » ... hms 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/. 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.
doi:10.1186/1471-2105-6-15 pmid:15663796 pmcid:PMC547898 fatcat:az3blh77ifa6doinrtch4cap4i