Essential genes are those whose presence is imperative for an organism’s survival, whereas the functions of non–essential genes may be useful but not critical. Abnormal functionality of essential genes may lead to defects or death at an early stage of life. Knowledge of essential genes is therefore key to understanding development, maintenance of m...
Heavy metal pollutants, discharged into the ecosystem as waste by anthropogenic activities, contaminate drinking water for millions of people and animals in many regions of the world. Long term exposure to these metals, leads to several lethal diseases like cancer, keratosis, gangrene, diabetes, cardio- vascular disorders, etc. Therefore, removal o...
Heavy metal pollutants, discharged into the ecosystem as waste by anthropogenic activities, contaminate drinking water for millions of people and animals in many regions of the world. Long term exposure to these metals, leads to several lethal diseases like cancer, keratosis, gangrene, diabetes, cardio- vascular disorders, etc. Therefore, removal o...
Published in BMC Genomics
BackgroundMany eukaryotes have been shown to use alternative schemes to the universal genetic code. While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as leucine, some yeasts, including many but not all of the “Candida”, translate the same codon as serine. It has been proposed tha...
Published in BMC Medical Genomics
BackgroundUnderstanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissu...
Published in PloS one
Aspirin-exacerbated respiratory disease (AERD) remains widely underdiagnosed in asthmatics, primarily due to insufficient awareness of the relationship between aspirin ingestion and asthma exacerbation. The identification of aspirin hypersensitivity is therefore essential to avoid serious aspirin complications. The goal of the study was to develop ...
Published in BMC Research Notes
BackgroundThe first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior ...
Published in BMC Research Notes
BackgroundThis paper proposes a method of implementing parallel gene prediction algorithms in MATLAB. The proposed designs are based on either Goertzel’s algorithm or on FFTs and have been implemented using varying amounts of parallelism on a central processing unit (CPU) and on a graphics processing unit (GPU).FindingsResults show that an implemen...
Published in BMC Genomics
BackgroundAs more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for...
Published in PLoS computational biology
Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consis...
