Background Unraveling the mechanisms that regulate gene expression is a major challenge
in biology. An important task in this challenge is to identify regulatory elements, especially …

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 …

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 …

Motivation: DNA motif finding is one of the core problems in computational biology, for which
several probabilistic and discrete approaches have been developed. Most existing methods …

Thoroughly Describes Biological Applications, Computational Problems, and Various
Algorithmic Solutions Developed from the author's own teaching material, Algorithms in …

Quality control is paramount in product manufacturing as it ensures consistent production to
meet customer expectations, regulatory requirements and maintain a company's reputation …

Pevzner and Sze [14] have introduced the Planted (l, d)-Motif Problem to find similar patterns
(motifs) in sequences which represent the promoter region of co-regulated genes. l is the …

In this paper, we study the problem of motif discoveries in unaligned DNA and protein
sequences. The problem of motif identification in DNA and protein sequences has been …

Many biological systems and objects are intrinsically fuzzy as their properties and behaviors
contain randomness or uncertainty. In addition, it has been shown that exact or optimal …

In this paper efficient exact algorithms are proposed for the planted (l, d)-motif search
problem. This problem is to find all motifs of length l that are planted in each input string with …