—We consider the problem of identifying motifs, recurring or conserved patterns, in the sets of biological sequences. To solve this task, we present new deterministic and exact a...
Background: Motif discovery aims to detect short, highly conserved patterns in a collection of unaligned DNA or protein sequences. Discriminative motif finding algorithms aim to i...
Quantification of selective pressures on regulatory sequences is a central question in studying the evolution of gene regulatory networks. Previous methods focus primarily on sing...
Background: False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a nume...
The history of molecular biology is punctuated by a series of discoveries demonstrating the surprising breadth of biological roles of ribonucleic acid (RNA). An ensemble of evoluti...