Journal
BMC BIOINFORMATICS
Volume 12, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2105-12-116
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Funding
- French Agence Nationale de la Recherche [NeMo ANR-08-BLAN-0304-01]
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Background: The number of gene sequences that are available for comparative genomics approaches is increasing extremely quickly. A current challenge is to be able to handle this huge amount of sequences in order to build families of homologous sequences in a reasonable time. Results: We present the software package SiLiX that implements a novel method which reconsiders single linkage clustering with a graph theoretical approach. A parallel version of the algorithms is also presented. As a demonstration of the ability of our software, we clustered more than 3 millions sequences from about 2 billion BLAST hits in 7 minutes, with a high clustering quality, both in terms of sensitivity and specificity. Conclusions: Comparing state-of-the-art software, SiLiX presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. SiLiX is freely available at http://lbbe.univ-lyon1.fr/SiLiX.
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