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Sequences lacking molecular function annotations have limited research value, so automated approaches for annotating molecular function are used to smooth over this deficiency. Whereas massive erroneous prediction results that may reduce the reliability and utility of these methods is non-ignorable in protein function prediction. Approaches combined phylogenomics and mathematical inference have been...
A complete open reading frame of htrA gene and its encoding protein of Haemophilus parasuis were analyzed by multiple bioinformatics software. The htrA gene was composed of 1380 bp nucleotides encoding HtrA protein of 459 amino acids. The molecular weight of the protein was 48494.4 Da with the formula C2140H3505N597O665S8. The HtrA protein had the following characteristics: one signal peptide cleavage...
In this paper, we present a new variations of the popular nonnegative matrix factorization (NMF) approach to extend it to the data with negative values. When a NMF problem is formulated as μ ≈μμ, we try to develop a new method that only allows μ to contain nonnegative values, but allows both μ and μ to have both nonnegative and negative values. In this way, the original NMF is extended to be used...
Since the introduction of next generation sequencing there is a demand for sophisticated methods to classify proteins based on sequence data. Two main approaches for this task are to use the raw sequence data and align them against other sequences, or to extract discrete high level features from the protein sequences and compare the features. Two machine learning methods are demonstrated to show each...
Pre-implantation embryonic development (PED) is an important early process in life. Two issues are emerged for PED study. First, malfunction of PED can lead to future problems such as intrauterine growth retardation and diabetes. Second, PED conservation and diversity between species can be used to interpret genetics questions of human and animal health as well as environment protection. One of the...
DNA sequences consist of four types of nucleotides, and converting the DNA sequence into a numerical sequence is an important task of the study of DNA sequences. In this paper, we propose an improved inter-nucleotide distances method which combines with Euclidean distance to analyze phylogenetic relationship of the 64 vertebrate complete mitochondrial genomes and construct corresponding phylogenetic...
To provide some insights into the understanding of the biological functions of tolC gene and its encoding protein in Actinobacillus pleuropneumoniae, multiple bioinformatics tools were employed to analyze the complete sequence of tolC gene and physicochemical properties, structure and functions of TolC protein of A. pleuropneumoniae. The results showed that tolC gene is a single open reading frame...
To pursue a new approach for discovering new side effects of drugs, we construct a drug-side effect network based on the SIDER2 database, and introducing link prediction methods in the network. We develop and evaluate the framework for drug side effect prediction based on link prediction in bipartite network. Integrating side effect appearance frequency has also been proved to be of value in improving...
Pearl gentian grouper, Epinephelus lanceolatus × Epinephelus fuscoguttatus, is a hybrid species with increasing market requirement in China. A disease outbreak occurred in the fish juvenile stages in Shandong Province, P.R. China. The gross signs were characterized by mass mortality, exhibiting dark skin coloration, reduce of feeding and having abnormal swimming behavior. Based on histopathological...
Predicting the structures of a protein, i.e. finding low-energy conformations of a protein is one of the most prominent problems in bioinformatics. A simplified two-dimensional (2D) hydrophobic-hydrophilic (HP) lattice model is studied. Despite the simplicity of the model, the protein structure prediction problem on the HP lattice model has been proven to be NP-hard. The ant colony optimization (ACO)...
Semiconductor quantum dots (QDs) have drawn considerable attention since its emergence because they have high brightness and a long luminous time. Our aim is to develop a new assay based on QDs to determine Alpha fetal protein (AFP) by immunofluorescence assay (IFA). Two different monoclonal antibodies of anti-AFP were labeled by QDs and the magnetic beads. After combination with AFP antigen, the...
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