Current Bioinformatics - Volume 9, Issue 2, 2014

Essential genes often play key roles in biological processes and mutations in these genes will have a great impact on an organism’s survival and reproduction. Studying lethal phenotypes will provide important information about the function of the gene product and direct gene therapy. Traditionally, essential genes have been identified through single-gene knockout experiments, transposon mutagenesis, or antisense RN Read More

Synonymous codon usage has long been known as a factor that affects the average expression level of proteins in microorganisms. A systematic approach to study the role of codon usage bias underlying gene expression has been described. Facts and ideas presented in this short review are to derive biological information from genome sequences by means of various statistical analyses and appropriate design of algorithms. Read More

The sequence similarity relationships between the members of a protein family contain information on its evolutionary history, such as the relative time of horizontal transfer events, and the differential acceleration or deceleration of evolution in particular organisms in response to selective pressures. This paper presents a quantitative representation and comparison of evolutionary profiles of proteins, and finds correlations Read More

The majority of viruses have a small genome. However, these small genomes often have complex gene features with transcriptional and translational exceptions, for instance, gene overlapping, alternative splicing, RNA editing, ribosomal slippage and stop codon read-through. These complex features and exceptions increase gene density and improve the gene coding efficiency of viral genomes. They also pose imme Read More

Rapid advances in gene expression microarray technology have enabled to discover molecular markers used for cancer diagnosis, prognosis, and prediction. One computational challenge with using microarray data analysis to create cancer classifiers is how to effectively deal with microarray data which are composed of high-dimensional attributes (p) and low-dimensional instances (n). Gene selection and classifier constructio Read More

More and more studies indicate that the issue of protein-coding gene finding in microbial genomes is far from thoroughly solved and the annotation quality has been questioned continuously in the past several years. In this paper, we summarize the computational methods for identifying the over-annotated genes and missing genes, and provide perspective for prospective gene finding works.

Driven by the rapid growth of the complete genome sequences, it is accepted that genome annotation has been resorted mostly to automatic methodology. For computational annotation to bacterial and archaeal genomes, accurate prediction of translation initiation sites (TISs) is essential to locate protein coding regions of genes. Therefore, TIS prediction has been a challenge to a number of gene finders and TIS processor Read More

Geobacter sulfurreducens PCA plays an important role in electricity production and bioremediation, as it can reduce uranium to an insoluble form, and uses organic compounds as electron donors. ATP-binding cassette (ABC) transporters are important as they regulate respiration and biofilm formation, which in turn affect the rate of electricity production and bioremediation. Thus we focused on identifying ABC transporters by Read More

For quite a while, the main focus of molecular biology has been on DNA, being the carrier of the genetic code, with RNA being viewed merely as an intermediary player. However, lately it has become obvious that RNA plays much more important roles in the cellular regulatory mechanisms. The discovery of various new types of RNA has provided a further boost to RNA research. As a result, research into small regulatory RNA mo Read More

Many aspects of the reproductive biology of scleractinian corals remain unknown. External fertilisation during broadcast spawning events generates the potential for interspecific hybridisation, yet whilst efficient cross-fertilisation often occurs in vitro and species boundaries are blurred due to introgression, in nature hybridisation happens rarely even between sympatric and highly cross-fertile species. One potential explanation Read More

Nucleosome positioning plays essential roles in various cellular processes. Although many efforts have been made in this area, the rules defining nucleosome positioning is still elusive. In the present study, DNA physical parameters derived from atomistic molecular dynamic simulations were introduced to analyze nucleosomal and linker DNA sequences. The distinct structural patterns between nucleosomal and linker sequence Read More

It is a great challenge to predict a protein structure and this challenge has fascinated researchers in different disciplines for many years. Basically the prediction process mainly includes two steps. With the first step that the generation of prediction model increasing fast, the second step that the quality estimation of predicted model i.e. identification of models’ native like structure becomes more and more important. In this st Read More

Uncovering the transcriptional regulation mechanism of mammalian miRNAs is crucial to understand the role of these tiny regulators in cellular processes. Based on 1,030 genomic and epigenetic functional annotations, we compared these features of regulatory regions between miRNAs and protein-coding genes. Support vector machine (SVM) was used to quantify the contribution of each annotation group or group combinati Read More