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Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Bioconductor version: Release (3.19)

Suffix Array Kernel Smoothing (see, or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.

Author: Dennis Wylie [aut, cre]

Maintainer: Dennis Wylie <denniscwylie at>

Citation (from within R, enter citation("sarks")):


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Reference Manual PDF


biocViews DifferentialExpression, FeatureExtraction, GeneExpression, GeneRegulation, MotifDiscovery, RNASeq, Software, Transcriptomics
Version 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License BSD_3_clause + file LICENSE
Depends R (>= 4.0)
Imports rJava, Biostrings, IRanges, utils, stats, cluster, binom
System Requirements Java (>= 1.8)
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