Current Bioinformatics - Volume 13, Issue 3, 2018

Microarray technology allows us to study the gene expression levels of thousands of genes over different experimental conditions in a single go. The gene expression data provided by microarray technology is of enormous size i.e. high dimensional which makes the downstream analysis a very challenging task. The gene selection is an essential process which removes the problem of dimensionality by removing irrelevant a Read More

Background: Most existing methods for comparing and analyzing DNA sequences use multiple sequence alignment (MSA) algorithms. However, the computation time required for MSA is usually very long and makes it impossible to analyze a large group of long DNA sequences. Objective: Here we propose a novel computational method to quickly characterize and compare DNA sequences. Method: We construct a new 2-dimensi Read More

Background: Error Correction is an important task in the analysis and manipulations of NGS data. The purpose of error correction is to facilitate data analysis for large projects like de novo assembly project. Here we present a new hybrid algorithm for error correction of long reads using short reads. Our algorithm can be flexibly adapted to different types of errors. Next, we make a de novo assembly for corrected long re Read More

Background: In the past decades, a number of methods are proposed for dealing with the classification of molecular data. Supervised ML methods such as linear discriminant analysis and decision trees were used to predict structural properties of molecules. Furthermore, logistic regression, Bayesian networks and artificial neural networks have been used to distinguish drugs and non-drugs. However, most of them can not hi Read More

Background: Intervening sequences (introns) have significant effects on genomic regulations and molecular evolution. So, it deserves a deeper analysis for better understanding the possible regulatory roles of these regions. Objective and Method: Accordingly, the intron 2 (In-2) of the human B-cell lymphoma 2 (hBcl2) gene, with regard to the size of the In-2 as well as critical roles of the gene in the homeostatic of the cellular Read More

Background: Depression is a serious mental ailment that is considered to be a global threat with an increased risk of prevalence. Drug development targeted against depression is an immense challenge as it encompasses multifaceted reasons with a poorly understood pathology along with the impediment of physiological blood brain barrier to the targeted site. Monoamine inhibitors are attainable as antidepressants since it has Read More

Background: To identify new bacterial type III secreted effectors is computationally a big challenge. At least a dozen machine learning algorithms have been developed, but so far have only achieved limited success. Sequence similarity appears important for biologists but is frequently neglected by algorithm developers for effector prediction, although large success was achieved in the field with this strategy a decade a Read More

Background: A robust guide tree is necessary as a first step for the multiple sequence alignment of proteins. The guide tree is normally generated using an initial distance matrix based on a particular distance metric. Objective: A new tool for generating guide trees for multiple protein sequence alignment is presented. Method: The algorithm involved in the initialization of the progressive algorithm for the alignment of sequences i Read More

Background: Mutation of EGFR is one of the most important drivers of non-small cell lung cancer. Many selective therapies take specific mutation of EGFR as target. For example, gefitinib is a commonly used front line drug for the mutations of exon 19 deletions and the L858R. New irreversible inhibitors, such as WZ4002, CO-1686, and AZD9291, are developed to overcome drug resistance caused by the acquired T790M mutatio Read More

Introduction: Dengue virus is among the most widespread mosquito-borne human pathogens with 5 different serotypes. A ratio of 3 to 7 structural and non-structural proteins is retained by the 10.7 kb viral RNA genome. The Dengue virus NS5, a non-structural and most conserved protein in the genome plays vital role in virus replication machinery. The C-terminal RNA-dependent RNA polymerase (RdRp) domain of NS5 has been Read More

Background: MicroRNAs (miRNA) are a class of non-coding single-strand small RNAs and play important roles against abiotic stress. High temperature is one of the major adversities that plants suffered during their growth and development. Objective: The research here was intended to profile the miRNAs in creeping bentgrass to characterize the possible heat resistance mechanisms. Method: Normal and 42132;ƒ high Read More