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Taxonomic annotation is a critical first step for analysis of metagenomic data. Despite a lot of tools being developed, the accuracy is still not satisfactory, in particular, when a close species-level reference does not exist in the database. In this paper, we propose a novel annotation tool, MetaAnnotator, to annotate metagenomic reads, which outperforms all existing tools significantly when only...
Classification of G protein-coupled receptors (GPCRs) according to their functions is an ongoing area of research which is helpful for the pharmaceutical industry in the development of drug targets for major diseases. Currently, more than 40% drugs in the market target GPCRs. The experimental methods of determining their function are very expensive and time consuming. Due to a rapid and constant increase...
Today, when comparing classical fingerprint matching and more constrained algorithms, like after binary quantization for biometric privacy protection purpose, there is an important gap in terms of performances. Performances of the latter solutions still need to be improved to decrease this gap. The main difficulty comes from the fact that fingerprint captures of the same trait give very different...
Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life, and a genome-scale metabolic network can be reconstructed by identifying, categorizing and interconnecting all the genes, proteins, reactions and metabolites that participate in the metabolic activity of a biological system to form a metabolic network. Enzymes play a very important part in metabolism,...
Protein glycosylation is one of the most common posttranslational modifications (PTMs) with several types. O-GlcNAcylation is an O-linked glycosylation with attachment of beta-N-acetylglucosamine (GlcNAc) to Ser/Thr residues catalyzed by O-GlcNAc transferase (OGA), whose removal is catalyzed by O-GlcNAcase. Unlike mucin-type O-glycosylation, O-GlcNAcylation occurs primarily in nucleocytoplasmic proteins...
In this paper, a prediction method of protein contact on the basis of information granules and RBF neural network have been brought forward. This method improved the encoding approach of protein structure data and classifier performance to enhance the predicting accuracy of protein contact. 200 nonhomologous proteins from the PDB database were encoded according to the encoding approach and were taken...
Protein function is highly correlated with its three dimensional conformation in order to interact with others proteins, ligands, substrates, inhibitors, etc. Studies on binding site and protein function have been investigated to understand the mechanism of protein activity; therefore, protein stability and flexibility play different roles on protein functions. In this work, we propose a framework...
We present a novel gene finding and validation tool, called GeneScope, which is capable of finding and validating genes declaratively by autonomously integrating heterogeneous online resources. GeneScope also supports user defined concepts to articulate gene structures, and refine existing concepts toward the discovery of the intended genes. The system relies upon a new string query language called...
Genomic sequencing projects are generating vast stores of data that provide opportunities and challenges in data analysis. Investigations of trends in codon usage have proven to be a rich area of study in this field. There are a number of methods for isolating codon usage bias in microbial organisms, each designed to capture a specific aspect of the bias. We posit that each species has evolved under...
The analysis of cellular behavior and functionality is the most challenging aim of systems biology. The extensive analysis of the interactions between different classes of intra-cellular molecules reacting to genetic/environment changes can elucidate the mechanisms of regulation involved on different cellular processes. We propose a novel framework that enables the integrated analysis of metabolic...
The paper presents an original, independent of typical cryptographic techniques, method of biometric replay attack prevention for iris biometrics. The proposed solution takes advantage of appropriate enhancements of iris templates and relies on appropriate data alteration within the image space resulting in significant changes of the resulting code in the iris feature space. Proposed methodology may...
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