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.

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Metadaten
Author:Antje Krause, Jens Stoye, Martin Vingron
URN:urn:nbn:de:kobv:526-opus-153
DOI:https://doi.org/10.15771/1471-2105_2005_6_15
DOI (Version of Record):https://doi.org/10.1186/1471-2105-6-15
ISSN:1471-2105
Parent Title (German):BMC Bioinformatics
Publisher:BioMed Central
Document Type:Article
Language:English
Year of Publication:2005
Publishing Institution:Technische Hochschule Wildau
Contributing Corporation:Max Planck Institut für molekulare Genetik, Abt. Computational Molecular Biology; Universität Bielefeld, Technische Fakultät, AG Genominformatik
Release Date:2007/07/05
Tag:Clusteralgorithmen; Hierarchisches Clustern; Protein; Proteinfamilie; Sequenz
cluster algorithms; hierarchical clustering; protein; protein family; sequence
Note:
zuerst bei BioMed Central Bioinformatics, Vol 6, 2005, publiziert. DOI 10.1186/1471-2105-6-15
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 3.0 DE - Namensnennung 3.0 Deutschland
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