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|Alternative name||CLUsters of SWISS-PROT and TREMBL proteins|
|Restrictions to use||None|
|Database management system||Oracle|
|User data submission||Not allowed|
Publication for CLUsters of SWISS-PROT and TREMBL proteins
GFam: a platform for automatic annotation of gene families
[…] 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 […]
Protein function annotation by homology based inference
[…] 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 […]
New developments in the InterPro database
[…] 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 […]
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
[…] 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, […]
Testing statistical significance scores of sequence comparison methods with structure similarity
[…] 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 […]
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
[…] 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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