Background There has been a growing interest in computational discovery of regulatory
elements, and a multitude of motif discovery methods have been proposed. Computational …

Proper development and functioning of an organism depends on precise spatial and
temporal expression of all its genes. These coordinated expression-patterns are maintained …

Serum response factor (SRF) binds a 1216-fold degenerate cis element known as the CArG
box. CArG boxes are found primarily in muscle-and growth-factor-associated genes …

The identification of regulatory regions is one of the most important and challenging
problems toward the functional annotation of the human genome. In higher eukaryotes …

Many functionally important regions of the genome can be recognized by searching for
sequence patterns, or ''motifs.''Aside from the genes themselves, examples include CpG …

The various organogenic programs deployed during embryonic development rely on the
precise expression of a multitude of genes in time and space. Identifying the cis-regulatory …

Regulation of gene expression in eukaryotic genomes is established through a complex
cooperative activity of proximal promoters and distant regulatory elements (REs) such as …

Determining how transcriptional regulatory signals are encoded in vertebrate genomes is
essential for understanding the origins of multicellular complexity; yet the genetic code of …

Identification and annotation of all the functional elements in the genome, including genes
and the regulatory sequences, is a fundamental challenge in genomics and computational …

Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods,
but also a key component in more advanced computational algorithms (eg, Gibbs sampler) …