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CluSTr specifications

Information


Unique identifier OMICS_24870
Name CluSTr
Alternative name CLUsters of SWISS-PROT and TREMBL proteins
Restrictions to use None
Database management system Oracle
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publication for CLUsters of SWISS-PROT and TREMBL proteins

CluSTr citations

 (7)
library_books

GFam: a platform for automatic annotation of gene families

2012
Nucleic Acids Res
PMCID: 3479161
PMID: 22790981
DOI: 10.1093/nar/gks631

[…] s between them are weighted with a measure related to the sequence similarity between the proteins. Clustering methods such as ProDom (), ProClust (), SYSTERS (), TribeMCL (), SCPS (, ), FORCE () and CluSTr () group proteins into families based on a set threshold of a sequence similarity measure [for instance, BLAST (,) E value or percent identity]; two protein sequences are considered potentially […]

library_books

Protein function annotation by homology based inference

2009
Genome Biol
PMCID: 2688287
PMID: 19226439
DOI: 10.1186/gb-2009-10-2-207

[…] milies from each other. An alternative approach to defining clusters is the construction of a tree representation that can provide a hierarchical view. Resources in this category include ProtoNet [], CluSTr [] and SYSTERS []. They are based on sequence similarities detected by an all-against-all sequence comparison, so that any level of evolutionary granularity can be inspected, from closely relat […]

library_books

New developments in the InterPro database

2007
Nucleic Acids Res
PMCID: 1899100
PMID: 17202162
DOI: 10.1093/nar/gkl841

[…] stracts.The ‘database links’ field has been extended to include new links to CluSTr and Pfam clans. lists the databases cross-referenced in InterPro and the number of entries containing these links. CluSTr () () is a database containing protein clusters from more than 368 organisms with completely sequenced genomes. The clustering is based on pairwise comparisons between the protein sequences. In […]

library_books

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

2006
Malar J
PMCID: 1665468
PMID: 17112376
DOI: 10.1186/1475-2875-5-110

[…] logues.A more CPU-demanding alternative method for massive all-against-all protein sequence comparison uses Smith-Waterman/Z-values rather than BlastP/E-values. This method has been initiated for the ClusTR protein sequence clustering, underlying the UniProt/Integr8 knowledge base at the European Bioinformatics Institute, EBI []. Because of the properties of the Z-value statistics detailed above, […]

library_books

Testing statistical significance scores of sequence comparison methods with structure similarity

2006
BMC Bioinformatics
PMCID: 1618413
PMID: 17038163
DOI: 10.1186/1471-2105-7-444

[…] o statistics, was introduced by Doolittle [] and implemented by Gene-IT [] in its sequence comparison suite Biofacet []. The Z-score has been used in the creation of the sequence annotation databases CluSTr [] and Protein World [] and was used in orthology studies []. The Z-score has also been implemented in algorithms other than Smith-Waterman, such as FASTA []. It is calculated by performing a n […]

library_books

JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture

2005
BMC Bioinformatics
PMCID: 1208858
PMID: 16135248
DOI: 10.1186/1471-2105-6-216

[…] hallenge.Several recent contributions addressed the clustering of very large sets of possibly unrelated protein sequences (e.g. TRIBE-MCL [], Picasso [], Systers [], COG [], ProtoMap [], ProtoNet [], ClusTr [] and ProClass []). All these approaches are based on pairwise or multiple alignments of the sequences to be analysed. Alternatively alignment-free sequence comparison methods were proposed ([ […]

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CluSTr institution(s)
EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
CluSTr funding source(s)
Supported in part by grant B104-CT97-2099 of the European Commission.

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