Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding
sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured …

The DNA motif discovery is a primary step in many systems for studying gene function. Motif
discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that …

Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA: RNA
hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect …

DNA/RNA motif mining is the foundation of gene function research. The DNA/RNA motif
mining plays an extremely important role in identifying the DNA-or RNA-protein binding site …

The DNA motif discovery (MD) problem is the main challenge of genome biology, and its
importance is directly proportional to increasing sequencing technologies. MD plays a vital …

Since the advent of systems and synthetic biology, many studies have sought to harness
microbes as cell factories through genetic and metabolic engineering approaches. Yeast …

Transcription factors are proteins that bind to specific DNA sequences and play important
roles in controlling the expression levels of their target genes. Hence, prediction of …

Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of
gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein …

A DNA motif is a sequence pattern shared by the DNA sequence segments that bind to a
specific protein. Discovering motifs in a given DNA sequence dataset plays a vital role in …

Background Given a set of tn-length DNA sequences, q satisfying 0< q≤ 1, and l and d
satisfying 0≤ d< l< n, the quorum planted motif search (qPMS) finds l-length strings that …