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 …

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for
finding motifs as ChIP-Seq experiments narrow down the motif finding to 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 …

Finding approximately conserved sequences, called motifs, across multiple DNA or protein
sequences is an important problem in computational biology. In this paper, we consider the …

Existing sequence mining algorithms mostly focus on mining for subsequences. However, a
large class of applications, such as biological DNA and protein motif mining, require efficient …

Background Motifs are patterns found in biological sequences that are vital for
understanding gene function, human disease, drug design, etc. They are helpful in finding …

Background Motif searching is an important step in the detection of rare events occurring in
a set of DNA or protein sequences. One formulation of the problem is known as (l, d)-motif …

ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation
parallel sequencing, allows for the genome-wide identification of protein-DNA interactions …

Discovering patterns in biological sequences is a crucial problem. For example, the
identification of patterns in DNA sequences has resulted in the determination of open …

Detection of rare events happening in a set of DNA/protein sequences could lead to new
biological discoveries. One kind of such rare events is the presence of patterns called motifs …