• FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

    10 days ago - By Oxford Journals

    AbstractSummaryAnalysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis...
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  • Bipartite tight spectral clustering algorithm for identifying conserved gene co-clusters in two species

    10 days ago - By Oxford Journals

    AbstractMotivationGene clustering is a widely used technique that has enabled computational prediction of unknown gene functions within a species. However, it remains a challenge to refine gene function prediction by leveraging evolutionarily conserved genes in another species. This challenge calls for a new computational algorithm to identify gene co-clusters in two species, so that genes in each co-cluster exhibit similar expression levels in each species and strong conservation between the species.ResultsHere, we develop the bipartite tight spectral clustering algorithm, which...
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