Current Bioinformatics - Volume 10, Issue 3, 2015

RNA structure prediction and structural motifs analysis are challenging tasks in the investigation of RNA function. We propose a novel procedure to detect structural motifs shared between two RNAs (a reference and a target). In particular, we developed two core modules: (i) nbRSSP_extractor, to assign a unique structure to the reference RNA encoded by a set of non-branching structures; (ii) SSD_finder, to detect structural mot Read More

Past decades have seen the rapid development of microarray technologies making available large amounts of gene expression data. Hence, it has become increasingly important to have reliable methods to interpret this information in order to discover new biological knowledge. In this review paper we aim to describe the main existing evolutionary methods that analyze microarray gene expression data by means of biclusterin Read More

Computational systems biology emphasizes on modeling biological systems mathematically and computationally for analyzing their role in solving complex processes. One of the applications of systems biology is understanding disease networks, for which various strategies such as, decisionmaking stochastic networks, graph theory based methods, robust control theory, elementary flux modes, extreme pathways, co Read More

Protein-protein interactions at membranes play an inevitable role in the function of proteins there. However, the task of studying the interactions is of many difficulties in case of the membrane proteins, due to their hydrophobic environment. This is why the use of bioinformatics methods, especially machine learning approaches is essential to understand the membrane proteins' function. However, the machine learning me Read More

Introduction: This is a first study where user friendly software (MASS KIR Analyzer) has been presented to analyze the Killer Immunoglobulin-like receptors (KIR) gene content diversity. The main objective of this software is to generate error free KIR genotyping data. Materials and Methods: The MASSKIR Analyzer accepts KIR genotyping data in binary format. It has the potential to determine KIR genotype, haplotype and link Read More

Operons, consisting of functionally related or correlated genes, are commonly found in prokaryotes and have enormous importance in understanding microbial genomics. To identify such genes, we developed a stand-alone tool (GAOPP) for predicting operons utilizing Genetic Algorithm approach. We also aimed to use minimum and easily available data set as input to obtain modest accuracy, and provide a gra Read More

It is well known that cancer is a highly heterogeneous disease, and the predictive capability of targeted gene signature approach suffers from the inter-tumor heterogeneity. Here we propose a framework to quantify the molecular heterogeneity of tumors from gene-gene relational perspective using co-expression networks and interactome data. We believe that to understand individualized gene behavior across patients, relatio Read More

In the field of drug research and development, the investigation of drug-drug interactions (DDIs) is a vital research area. Many clinical tools are used in the industry providing the broad lists of DDIs. But these tools can return unpredictable results, only limited to specific types of interaction. Also these tools lack the synchronized database of drug-drug interaction. In our research work, we are proposing a novel pattern recogn Read More

Plant cell contains two major cell organelles, chloroplast and mitochondria, which play key roles in energy metabolism as well as in regulating a number of prominent processes. Also, proteins that are located in both chloroplast and mitochondria presumably function distinctly in both locations, and therefore the knowledge about the localization of protein is vital. Hence, a webserver (DualPred) is designed to predict th Read More

An improved mathematical object is presented for analyzing the similarity and dissimilarity of DNA sequences. The kernel of it is to employ the changes of the x-coordinates and y-coordinates of the points corresponding to the bases of DNA sequence in the method of graphical representation, respectively. Compared with the traditional methods based on the distances between points, a more detailed considerati Read More

Nucleotide evolution models benefit a lot from the reported neighbor-dependent nucleotide mutations. Investigations of neighboring-site effects of amino acid substitutions may also promote the development of protein evolution models. Here, the neighboring-site effects of amino acid substitutions in the mouse genome are evaluated by grouping the 20 amino acids into four categories: nonpolar neutral (NON), polar ne Read More