Many proteins of the Rel family can act as both transcriptional activators and repressors. However, mechanism that discerns the 'activator/repressor' functions of Rel-proteins such as Dorsal (Drosophila homologue of mammalian NFκB) is not understood. Using genomic, biophysical and biochemical approaches, we demonstrate that the underlying principle of this functional specificity lies in the 'se...

Currently, there are a number of motif detection tools available that possess unique functionality. These tools often report different motifs, and therefore use of multiple tools is generally advised since common motifs reported by multiple tools are more likely to be biologically significant. However, results produced by these different tools need to be compared and existing similarity detecti...

Cell-surface display is the expression of peptides and proteins on the surface of living cells by fusing them tofunctional components of cells which are exposed to the environment of cells. This strategy can be carriedout using different surface proteins of cells as anchoring motifs and different proteins from different sourcesas a passenger protein. It is a promising strategy...

Noncanonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols u...

Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins in...

Given a functionally heterogeneous group of proteins, such as a large superfamily, or an entire database, two important problems in biology are the automated inference of subsets of functionally related proteins and the identification of functional regions and residues. The former is typically performed in an unsupervised bottom-up manner, by clustering based on pairwise sequence similarity. Th...

The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revi...

RNA stem-loop structures play an important role in almost every step of the viral replication cycle. In this contribution, a mathematical analysis is performed on large dataset secondary structure elements coding regions viruses by using topological indices that capture Laplacian eigenvalues associated graph representations and thereby enable structural classification, supplemented folding ener...