Current Bioinformatics - Volume 2, Issue 3, 2007

Gene expression data are essential in understanding gene functions, biological networks, and cellular conditions. Over the last decade, with the use of DNA microarray technology, larger-scale gene expression data has become available and various data mining techniques have been used in an attempt to extract biologically relevant knowledge. Rule mining is a widely used approach in data mining and lately has attracted consid Read More

Protein structures are classically described as composed of two regular states, the α-helices and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple definition of secondary structures hides numerous limitations. In fact, the rules for secondary structure assignment are complex. Thus, numerous assignment methods based on different criteria have emerged leading to heterogeneous and Read More

Various gene expression DNA microarray platforms have been developed and often similar experiments are conducted using different types of arrays. Several investigators have explored the cross-platform comparison issues and reached mixed conclusions, ranging from discrepant to reasonably concordant results across platforms. These comparative studies, however, did not apply rigorous sequence-matching criteri Read More

Molecular characterization of various microbial genomes has revealed that many pathogenic and mutualistic intracellular bacterial species have smaller genomes than their free-living relatives. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Obligatory intracellular parasites display marked similarities in patterns of protein length and frequency distribution, wi Read More

Ets family transcription factors, characterized by an evolutionary conserved Ets domain, play important roles in cell development, cell differentiation, apoptosis and tissue remodeling. All members of this family have an activation or a repression domain for DNA binding. The Ets domain has been shown to bind 5'-GGAA/T-3' core motif of DNA by its wHTH (winged helix-turn-helix) structure, as determined by NMR o Read More