Proteins, such as many transcription factors, that bind to specific DNA sequences are
essential for the proper regulation of gene expression. Identifying the specific sequences …

The specificity of protein-DNA interactions is most commonly modeled using position weight
matrices (PWMs). First introduced in 1982, they have been adapted to many new types of …

We describe the comprehensive characterization of homeodomain DNA-binding specificities
from a metazoan genome. The analysis of all 84 independent homeodomains from D …

Finding where transcription factors (TFs) bind to the DNA is of key importance to decipher
gene regulation at a transcriptional level. Classically, computational prediction of TF binding …

Proteins with sequence-specific DNA binding function are important for a wide range of
biological activities. De novo prediction of their DNA-binding specificities from sequence …

Abstract Man and Stormo and Bulyk et al. recently presented their results on the study of the
DNA binding affinity of proteins. In both of these studies the main conclusion is that the …

Abstract enoLOGOS is a web-based tool that generates sequence logos from various input
sources. Sequence logos have become a popular way to graphically represent DNA and …

Relatively little is known about the mechanisms through which gene expression regulation
evolves. To investigate this, we systematically explored the conservation of regulatory …

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 …

Cys2His2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding
domains. Despite this domain's well-defined DNA-recognition interface, and its successful …