ArticleBMC bioinformatics2005
Large scale hierarchical clustering of protein sequences.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering.Molecular biology and evolution · 2025Article
- Fine-tuning of conditional Transformers improvesComputational and structural biotechnology journal · 2025Article
- Catching the π-Stacks: Prediction of Aggregate Structures of Porphyrin.The journal of physical chemistry. A · 2024Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.PLoS computational biology · 2017Article
- Article
- Clustering analysis of proteins from microbial genomes at multiple levels of resolution.BMC bioinformatics · 2016Article
- Topological analysis of the Escherichia coli WcaJ protein reveals a new conserved configuration for the polyisoprenyl-phosphate hexose-1-phosphate transferase family.Scientific reports · 2015Article
- Massive fungal biodiversity data re-annotation with multi-level clustering.Scientific reports · 2014Article
- Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes.BMC genomics · 2012Article
- GFam: a platform for automatic annotation of gene families.Nucleic acids research · 2012Article
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
- Application of clustering analyses to the diagnosis of Huntington disease in mice and other diseases with well-defined group boundaries.Computer methods and programs in biomedicine · 2011Article
- Article
- Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information.BMC genomics · 2011Article
- Comprehensive cluster analysis with Transitivity Clustering.Nature protocols · 2011Article
- Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.PloS one · 2011Article
- Genome-wide comparative gene family classification.PloS one · 2010Article
- Family classification without domain chaining.Bioinformatics (Oxford, England) · 2009Article
- Partitioning clustering algorithms for protein sequence data sets.BioData mining · 2009Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSearching 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.
resultsWe 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/.
conclusionsComparisons 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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