Cluster-C

 swMATH ID: 10932 Software Authors: Mohseni-Zadeh, S.; Brézellec, P.; Risler, J.-L. Description: Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques Although the characterization of proteins cannot solely rely upon sequence similarity, it has been widely proved that all-vs-all massive sequence comparisons may be an effective approach and a good basis for the prediction of biochemical functions or for the delineation of common shared properties. The program Cluster-C presented here enables a stand-alone and efficient construction of protein families within whole proteomes. The algorithm, which is based on the detection of cliques, ensures a high level of connectivity within the clusters. As opposed to the single transitive linkage method, Cluster-C allows a large number of sequences to be classified in such a way that the multidomain proteins do not produce a chain-grouping effect resulting in meaningless clusters. Moreover, some proteins can be present in several different but relevant clusters, which is of help in the determination of their functional domains. In the present analysis we used the $$Z$$-value, an evaluation of the significance of the similarity score, as the criterion for connecting sequences (the user can freely define the threshold of the similarity criterion). The clusters built with a rather low threshold ($$Z$$=14) include more than 97 Homepage: http://www.sciencedirect.com/science/article/pii/S1476927104000386 Keywords: Protein clustering; Maximal clique; Multidomain proteins; Sequence similarity Related Software: BLAST; PSI-BLAST; Algorithm 457; MrBayes; ProClust; MEGA; PHYLIP; Pajek; GenThreader; Pfam; FUGUE; RAPTOR; GeneRAGE; LASSAP Cited in: 6 Publications
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Cited by 18 Authors

 1 Błażewicz, Jacek 1 Brézellec, Pierre 1 Chang, Lijun 1 Dai, Qi 1 Dubois, Didier 1 Liu, Xiaoqing 1 Łukasiak, Piotr 1 Miłostan, Maciej 1 Mohseni-Zadeh, S. 1 Qin, Lu 1 Risler, J.-L. 1 Sánchez, Daniel Eduardo 1 Takahashi, Haruhisa 1 Tanaka, Akira 1 Tomita, Etsuji 1 Yao, Yuhua 1 Yu, Jeffrey Xu 1 Zhao, Fukun

Cited in 5 Serials

 1 Theoretical Computer Science 1 Algorithmica 1 Annals of Operations Research 1 Computational Biology and Chemistry 1 Journal of Theoretical Biology

Cited in 5 Fields

 3 Biology and other natural sciences (92-XX) 2 Combinatorics (05-XX) 1 Statistics (62-XX) 1 Computer science (68-XX) 1 Operations research, mathematical programming (90-XX)