Large scale hierarchical clustering of protein sequences
- 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.
| URN: | urn:nbn:de:kobv:526-opus-153 |
|---|---|
| DOI: | https://doi.org/10.15771/1471-2105_2005_6_15 |
| Publisher DOI: | https://doi.org/10.1186/1471-2105-6-15 |
| Author: | Antje Krause, Jens StoyeORCiD, Martin VingronORCiD |
| ISSN: | 1471-2105 |
| Parent Title (German): | BMC Bioinformatics |
| Document Type: | Article |
| Language: | English |
| Year of Publication: | 2005 |
| Publisher: | BioMed Central |
| Publishing Institution: | Technische Hochschule Wildau |
| Tag: | Clusteralgorithmus; Hierarchisches Clustern; Protein; Proteinfamilie; Sequenz cluster algorithm; hierarchical clustering; protein; protein family; sequence |
| Source: | Krause, A., Stoye, J. & Vingron, M. Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 6, 15 (2005). https://doi.org/10.1186/1471-2105-6-15 |
| Faculties an central facilities: | Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014) |
| Dewey Decimal Classification: | 0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik |
| Licence (German): |  Creative Commons - CC BY - Namensnennung 2.0 Generic |
| Release Date: | 2007/07/05 |
