Finding composite regulatory patterns in DNA sequences

By Eleazar Eskin, Pavel A. Pevzner. Intelligent Systems in Molecular Biology, 2002

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Computational prediction of transcription-factor binding site locations (2003, background): “expression of the nearby gene(s) [71], a number of approaches have been developed to identify pairs of binding sites [72-78].”
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps (2015, methodology): “[33, 34]), and methods like Weeder and MITRA organized efficient searches for enriched k-mers and composite k-mer patterns, respectively, using traversal of suffix tree or retrieval tree data structures to count occurrences of k-mer occurrences with inexact matches [35, 36].”
Combining phylogenetic data with co-regulated genes to identify regulatory motifs (2003, methodology): “Over the past few years, several algorithms have been developed for this purpose, including Gibbs sampler (Lawrence et al ., 1993), Consensus (Stormo and Hartzell, 1989; Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994, 1995), ANN-Spec (Workman and Stormo, 2000), AlignACE (Hughes et al ., 2000)”
A survey of DNA motif finding algorithms (2007, background): “[34] and Eskin and Pevzner [35] respectively, are also based on the suffix tree and its variant.”