The goal for this section of the course is to characterize families of related DNA or protein sequences. We may be interested in characterizing sequence surrounding binding sites of particular proteins, promoter regions, the location of genes, exons, or splice junctions in DNA sequence, families of repeated sequences, or families of proteins with similar function. Methods presented in this sect...

Visual motifs are images of visual experiences that are significant and shared across many people, such as an image of an informative sign viewed by many people and that of a familiar social situation such as when interacting with a clerk at a store. The goal of this study is to discover visual motifs from a collection of first-person videos recorded by a wearable camera. To achieve this goal, ...

The purpose of motif discovery as discussed here is to find binding sites of DNA binding regulators. We assume that the binding sites are short segments of DNA, not necessarily contiguous, to which a specific (family of) transcription factors can bind. While such sites may appear in genic as well as inter­genic regions, we focus here on finding binding sites only in the promoter region of each ...

This paper introduces the first integrated algorithm designed to discover novel motifs in heterogeneous sequence data, which is comprised of coregulated genes from a single genome together with the orthologs of these genes from other genomes. Results are presented for regulons in yeasts, worms, and mammals.

In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 . . . gm is a string of m characters. In each background sequence is implanted a probabilistically-ge...

Motif discovery is one of the most challenging problems in bioinformatics today. DNA sequence motifs are becoming increasingly important in analysis of gene regulation. Motifs are short, recurring patterns in DNA that have a biological function. For example, they indicate binding sites for Transcription Factors (TFs) and nucleases. There are a number of Motif Discovery algorithms that run seque...