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Genome-Wide Identification and Comparative Analysis of Copper Transporter Genes in Plants
In this study, a total of 78 potential Cu transporter genes were identified from 18 different plant species. Study revealed that Cu transporters could be characterized with a CTR protein family (PF04145) domain, three putative transmembrane domains (TMDs), a single exon number, and a basic character. Met-rich motifs at N-terminal region, MXXXM motif in TMD-2, and GXXXG motif in TMD-3 could be essential for Cu transport since they were highly conserved in all analyzed species. In phylogeny, a clear distinction was observed between Cu transporter sequences of lower and higher plants. General topological features of Cu transp...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 8, 2016 Category: Bioinformatics Source Type: research

Herbal Lead as Ideal Bioactive Compounds Against Probable Drug Targets of Ebola Virus in Comparison with Known Chemical Analogue: A Computational Drug Discovery Perspective
This study serves to bestow paramount information for further experimental studies concerning the utility of herbal ligands as probable lead molecules against Ebola viral targets. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - February 8, 2016 Category: Bioinformatics Source Type: research

Unwinding the Novel Genes Involved in the Differentiation of Embryonic Stem Cells into Insulin-Producing Cells: A Network-Based Approach
Abstract Diabetes is one of the main causes of death in the world. Diabetes is marked by high blood glucose levels and develops when the body doesn’t produce enough insulin or is not able to use insulin effectively, or both. Type I diabetes is a chronic sickness caused by lack of insulin due to the autoimmune destruction of pancreatic insulin-producing beta cells. Research on permanent cure for diabetes is in progress with several remarkable findings in the past few decades among which stem cell therapy has turned out to be a promising way to cure diabetes. Stem cells have the remarkable potential to differe...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 8, 2016 Category: Bioinformatics Source Type: research

PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study
Abstract Online retrieval of the homologous nucleotide sequences through existing alignment techniques is a common practice against the given database of sequences. The salient point of these techniques is their dependence on local alignment techniques and scoring matrices the reliability of which is limited by computational complexity and accuracy. Toward this direction, this work offers a novel way for numerical representation of genes which can further help in dividing the data space into smaller partitions helping formation of a search tree. In this context, this paper introduces a 36-dimensional Periodicity C...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 29, 2016 Category: Bioinformatics Source Type: research

Structural Interactions of Curcumin Biotransformed Molecules with the N-Terminal Residues of Cytotoxic-Associated Gene A Protein Provide Insights into Suppression of Oncogenic Activities
Abstract Curcumin as a natural product has drawn considerable attention in recent years for its multiple pharmacological activities against various diseases, but more studies are required to understand the curcumin pharmacological action considering its low bioavailability. Though numerous reasons contribute to the low bioavailability of curcumin, one of the important reasons is associated with biotransformation of curcumin through either conjugation or reduction depending on curcumin administration route. The orally administered curcumin (CUR) is metabolised into curcumin glucuronidase (CUR-GLR) and curcumin sulp...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 21, 2016 Category: Bioinformatics Source Type: research

A New Decision Tree to Solve the Puzzle of Alzheimer’s Disease Pathogenesis Through Standard Diagnosis Scoring System
Abstract Alzheimer’s disease (AD) is a progressive, incurable and terminal neurodegenerative disorder of the brain and is associated with mutations in amyloid precursor protein, presenilin 1, presenilin 2 or apolipoprotein E, but its underlying mechanisms are still not fully understood. Healthcare sector is generating a large amount of information corresponding to diagnosis, disease identification and treatment of an individual. Mining knowledge and providing scientific decision-making for the diagnosis and treatment of disease from the clinical dataset are therefore increasingly becoming necessary. The curr...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 20, 2016 Category: Bioinformatics Source Type: research

Molecular Characterization and Antimicrobial Activity of an Endolichenic Fungus, Aspergillus sp. Isolated from Parmelia caperata of Similipal Biosphere Reserve, India
Abstract Endolichenic fungi are microbes that inhabit healthy inner lichen tissues without any disease symptoms. They have been reported to produce new and interesting bioactive metabolites. In the present study, an endolichenic fungus frequently isolated from surface-sterilized lichen thallus of Parmelia caperata has been described. The fungus was identified as Aspergillus tubingensis based on morphological traits and ITS rDNA sequence. Crude metabolites extracted from the culture broth exhibited considerable antimicrobial activity against a panel of clinically significant human path...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 20, 2016 Category: Bioinformatics Source Type: research

Comparative Modeling, Molecular Docking, and Revealing of Potential Binding Pockets of RASSF2; a Candidate Cancer Gene
Abstract RASSF2, potential tumor suppressor gene, acts as a KRAS-specific effectors protein and may promote apoptosis and cell cycle arrest. It stabilizes STK3/MST2 by protecting it from proteasomal degradation. RASSF2 plays a significant role against the inhibition of cancer. MODELLER (9v15) and online servers (I-Tasser, SwissModel, 3D-JigSaw, ModWeb) were utilized to generate 3D structures of the RASSF2 based on homology modeling. A comparison between models predicted by MODELLER (9v15) and Web servers had been checked through utilized evaluation tools. The most potent model for RASSF2 was analyzed and selected ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 18, 2016 Category: Bioinformatics Source Type: research

ConnectViz : Accelerated Approach for Brain Structural Connectivity Using Delaunay Triangulation
This study proposes an accelerated approach for brain connectomic visualization based on graph theory paradigm using compute unified device architecture, extending the previously proposed SurLens Visualization and computer aided hepatocellular carcinoma frameworks. The accelerated brain structural connectivity framework was evaluated with stripped brain datasets from the Department of Surgery, University of North Carolina, Chapel Hill, USA. Significantly, our proposed framework is able to generate and extract points and edges of datasets, displays nodes and edges in the datasets in form of a network and clearly maps data v...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Structural Requirements of Some 2-(1-Propylpiperidin-4-yl)-1H-benzimidazole-4-carboxamide Derivatives as Poly (ADP-Ribose) Polymerase (PARP) for the Treatment of Cancer: QSAR Approach
Abstract The present study is aimed to elucidate the structural features of substituted 2-(1-propylpiperidin-4-yl)-1H-benzimidazole-4-carboxamide required for poly (ADP-ribose) polymerase inhibition and to obtain predictive 2D QSAR models to guide the rational synthesis of novel poly (ADP-ribose) polymerase inhibitors. The statistical analysis has shown that excellent results are obtained by using partial least regression based on simulated annealing method. The best model was selected based on the highest correlation coefficient r 2 = 0.8590, and cross-validated squared correlation coeff...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

In Silico Elucidation and Inhibition Studies of Selected Phytoligands Against Mitogen-Activated Protein Kinases of Protozoan Parasites
Abstract Parasitic MAPKs exhibiting significant divergence with humans and playing an imperative role in parasitic metabolic activities have been exploited from several years as important targets for development of novel therapeutics. In addition, the emergence of the drug-resistant variants of parasitic diseases in the recent years has aroused a great need for the development of potent inhibitors against them. In the present study, we selected the metabolically active MAPKs LmxMPK4, PfMAP2 and TbMAPK5 of the three parasitic protozoans Leishmania mexicana, Plasmodium falciparum and Trypanosoma brucei, respectivel...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

A Structure–Activity Relationship Study of Imidazole-5-Carboxylic Acid Derivatives as Angiotensin II Receptor Antagonists Combining 2D and 3D QSAR Methods
Abstract Two-dimensional (2D) and three-dimensional (3D) quantitative structure–activity relationship (QSAR) studies were performed for correlating the chemical composition of imidazole-5-carboxylic acid analogs and their angiotensin II $$\hbox {AT}_{1}$$ receptor antagonist activity using partial least squares and k-nearest neighbor, respectively. For comparing the three different feature selection methods of 2D-QSAR, k-nearest neighbor models were used in conjunction with simulated annealing (SA), genetic algorithm and stepwise coupled with partial least ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

PGWD: Integrating Personal Genome for Warfarin Dosing
Abstract Warfarin is a drug normally used in the prevention of thrombosis and the formation of blood clots. The dosage of warfarin is strongly affected by genetic variants of CYP2C9 and VKORC1 genes. Current technologies for detecting the variants of these genes are mainly based on real-time PCR. In recent years, due to the rapidly dropping cost of whole genome sequencing and genotyping, more and more people get their whole genome sequenced or genotyped. However, current software for warfarin dosing prediction is based on low-throughput genetic information from either real-time PCR or melting curve methods. There...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Computational Analysis and In silico Predictive Modeling for Inhibitors of PhoP Regulon in S. typhi on High-Throughput Screening Bioassay Dataset
Abstract There is emergence of multidrug-resistant Salmonella enterica serotype typhi in pandemic proportions throughout the world, and therefore, there is a necessity to speed up the discovery of novel molecules having different modes of action and also less influenced by the resistance formation that would be used as drug for the treatment of salmonellosis particularly typhoid fever. The PhoP regulon is well studied and has now been shown to be a critical regulator of number of gene expressions which are required for intracellular survival of S. enterica and pathophysiology of disease like typhoid. The evident ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Comparative Analysis of the Molecular Adjuvants and Their Binding Efficiency with CR1
Abstract There are so many obstacles in developing a vaccine or vaccine technology for diseases like cancer and human immunodeficiency virus infection. While developing vaccines that target specific infection, molecular adjuvants are indispensable. These molecular adjuvants act as a vaccine delivery vehicle to the immune system to increase the effectiveness of the specific antigens. In the present work, a computational study has been done on molecular adjuvants like IgGFc, GMCSF and C3d to find out how efficiently they are binding to CR1. Sequence, structure and mutational analysis are performed on the molecu...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Characteristics Analyses and Comparisons of the Protein Structure Networks Constructed by Different Methods
Abstract Protein structure networks (PSNs) were widely used in analyses of protein structure and function. In this work, we analyzed and compared the characters of PSNs by different methods. The degrees of the different types of the nodes were found to be associated with the amino acid characters, including SAS, secondary structure, hydropathy and the volume of amino acids. It showed that PSNs by the methods of CA10, SC10 and AT5 inherited more amino acid characters and had higher correlations with the original protein structures. And PSNs by these three methods would be powerful tools in understanding the charac...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

A Complete and Accurate Ab Initio Repeat Finding Algorithm
Abstract It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index a...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Effects of Different Carbon Sources on Growth, Membrane Permeability, β-Sitosterol Consumption, Androstadienedione and Androstenedione Production by Mycobacterium neoaurum
Abstract Effects of different carbon sources on growth, membrane permeability, β-sitosterol consumption, androstadienedione and androstenedione (AD(D)) production by Mycobacterium neoaurum were investigated. The results indicated that glucose was advantageous to the growth and resulted in the adverse effects on the phytosterols consumption and AD(D) production compared to the results of propanol and isopropanol as sole carbon source. The cell wall widths of 9.76 by propanol and 8.00 nm by isopropanol were 38.3 and 49.4 % thinner than that of 15.82 nm by glucose, respectively. The partition coe...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment
Abstract Space complexity is a million dollar question in DNA sequence alignments. In this regard, memory saving under pushdown automata can help to reduce the occupied spaces in computer memory. Our proposed process is that anchor seed (AS) will be selected from given data set of nucleotide base pairs for local sequence alignment. Quick splitting techniques will separate the AS from all the DNA genome segments. Selected AS will be placed to pushdown automata’s (PDA) input unit. Whole DNA genome segments will be placed into PDA’s stack. AS from input unit will be matched with the DNA genome segments f...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 14, 2016 Category: Bioinformatics Source Type: research

Hammerhead Ribozymes in Archaeal Genomes: A Computational Hunt
This study reveals a very scarce presence of HHRs in Archaea which suggests the involvement of other ncRNA elements in gene regulatory system like RNase P which are abundantly found in the Archaeal domain. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - January 13, 2016 Category: Bioinformatics Source Type: research

An Approach for Identification of Novel Drug Targets in Streptococcus pyogenes SF370 Through Pathway Analysis
Abstract Streptococcus pyogenes is one of the most important pathogens as it is involved in various infections affecting upper respiratory tract and skin. Due to the emergence of multidrug resistance and cross-resistance, S. Pyogenes is becoming more pathogenic and dangerous. In the present study, an in silico comparative analysis of total 65 metabolic pathways of the host (Homo sapiens) and the pathogen was performed. Initially, 486 paralogous enzymes were identified so that they can be removed from possible drug target list. The 105 enzymes of the biochemical pathways of S. pyogenes from the KEGG ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 11, 2016 Category: Bioinformatics Source Type: research

Computational Approach for Securing Radiology-Diagnostic Data in Connected Health Network using High-Performance GPU-Accelerated AES
This study proposes a secured radiology-diagnostic data framework for connected health network using high-performance GPU-accelerated Advanced Encryption Standard. The study was evaluated with radiology image datasets consisting of brain MR and CT datasets obtained from the department of Surgery, University of North Carolina, USA, and the Swedish National Infrastructure for Computing. Sample patients’ notes from the University of North Carolina, School of medicine at Chapel Hill were also used to evaluate the framework for its strength in encrypting–decrypting textual data in the form of medical report. Signifi...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 11, 2016 Category: Bioinformatics Source Type: research

Design, Synthesis, Spectral Analysis, In Vitro Anticancer Evaluation and Molecular Docking Studies of Some Fluorescent 4-Amino-2, 3-Dimethyl-1-Phenyl-3-Pyrazolin-5-One, Ampyrone Derivatives
Abstract The commenced work deals with the synthesis, characterization and evaluation of biological activities of 4-amino-2,3-dimethyl-1-phenyl-3-pyrazolin-5-one. The synthesis was done by the condensation of aromatic acid chlorides with 4-aminoantipyrine. The structures of synthesized derivatives were elucidated using IR, Mass, 1H NMR and 13C NMR spectroscopy, and their UV–Visible and fluorescence properties were studied. The compounds showed significant dual fluorescence. Molecular docking was used to understand the small molecule–receptor protein interaction. The derivatives were screened for their ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 2, 2016 Category: Bioinformatics Source Type: research

Interaction of Quercetin of Onion with Axon Guidance Protein Receptor, NRP-1 Plays Important Role in Cancer Treatment: An In Silico Approach
Abstract Neuropilin-1 (NRP-1) is a transmembrane glycoprotein receptor whose distinct sites bind semaphorins and vascular endothelial growth factor family members to mediate the role of these ligands in neuronal axon guidance and angiogenesis, respectively. Similarly, Eph receptors and ephrin ligands play critical roles in various biological functions, and deregulated activation of Eph/ephrin signaling in humans is thought to lead to tumorigenesis. Therefore, in this paper, an attempt was made to elucidate the inhibition potential of nine bioactive compounds from four different native spices of Bangladesh against ...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 26, 2015 Category: Bioinformatics Source Type: research

Prediction of Type II Toxin-Antitoxin Loci in Klebsiella pneumoniae Genome Sequences
Abstract Klebsiella pneumoniae is an increasingly important bacterial pathogen to human. This Gram-negative bacterium species has become a serious concern due to its dramatic increase in the levels of multiple antibiotic resistances, particularly to carbapenems. The toxin-antitoxin (TA) system has recently been reported to be involved in the formation of drug-tolerant persister cells. The type II TA system is composed of a stable toxin protein and a relatively unstable antitoxin protein that is able to inhibit the toxin. Here, we examine the type II TA locus distribution and compare the TA diversity...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 10, 2015 Category: Bioinformatics Source Type: research

Classification and Functional Analyses of Putative Conserved Proteins from Chlamydophila pneumoniae CWL029
Abstract Chlamydophila pneumoniae, a Gram-negative bacterium belongs to the family Chlamydiaceae, is known to cause community-acquired pneumonia and bronchitis. There is a need for genomic analyses of C. pneumoniae as its chronic infections result in reactive airway disease, lung cancer and asthma. Recent advancement in the sequencing techniques led to the generation of large genomic data. In order to utilize these data, sequence-based function predictions were used for annotating the uncharacterized genes. The genome of C. pneumoniae encodes 1052 proteins, which include a group of 366 functionally ...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 9, 2015 Category: Bioinformatics Source Type: research

Evaluating Left-Censored Data Through Substitution, Parametric, Semi-parametric, and Nonparametric Methods: A Simulation Study
In this study, an attempt was made to determine the degrees of bias in particular sampling sizes and methods. The aim of the study was to determine deviations from the median, the mean, and the standard deviation (SD) in different sample sizes and at different censoring rates for log-normal, exponential, and Weibull distributions in the case of full and censored data sampling. Thus, the concept of “censoring” and censoring types was handled in the first place. Then substitution, parametric (MLE), nonparametric (KM), and semi-parametric (ROS) methods were introduced for the evaluation of left-censored observatio...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 21, 2015 Category: Bioinformatics Source Type: research

Prospective QSAR-Based Prediction Models with Pharmacophore Studies of Oxadiazole-Substituted $$\alpha$$ α -Isopropoxy Phenylpropanoic Acids with Dual Activators of PPAR $$\alpha$$ α and PPAR $$\gamma$$ γ
Abstract A series of oxadiazole-substituted $$\alpha$$ -isopropoxy phenylpropanoic acids with dual activators of PPAR $$\alpha$$ and PPAR $$\gamma$$ derivatives were subjected to two-dimensional and k-Nearest Neighbors molecular field analysis. The statistically significant best 2D-QSAR (PPAR $$\alpha$$ ) model having good predictive ability with statistical values of $$r^{2} = 0.8725, \,q^{2... Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein Abstract Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region... Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research A Structure–Activity Relationship Study of Naphthoquinone Derivatives as Antitubercular Agents Using Molecular Modeling Techniques Abstract Tuberculosis (TB) is one of the major causes of death worldwide. Mycobacterium tuberculosis, the leading causative agent of TB, is responsible for the morbidity and mortality of a large population worldwide. In view of above and as a part of our effort to develop new and potent anti-TB agents, a series of substituted naphthoquinone derivatives were subjected to molecular modeling using various feature selection methods. The statistically significant best 2D-QSAR model having correlation coefficient \(r^{2} = 0.8643$$ and cross-validated squared correlati...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

In Silico Analysis of Sequence–Structure–Function Relationship of the Escherichia coli Methionine Synthase
Abstract The molecular evolution of various metabolic pathways in the organisms can be employed for scrutinizing the molecular aspects behind origin of life. In the present study, we chiefly concerned about the sequence–structure–function relationship between the Escherichia coli methionine synthase and their respective animal homologs by in silico approach. Using homology prediction technique, it was observed that only 79 animal species showed similarity with the E. coli methionine synthase. Also, multiple sequence alignment depicted only 25 conserved patterns between the E. coli methionine synthase ...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

A Massively Parallel Computational Method of Reading Index Files for SOAPsnv
Abstract SOAPsnv is the software used for identifying the single nucleotide variation in cancer genes. However, its performance is yet to match the massive amount of data to be processed. Experiments reveal that the main performance bottleneck of SOAPsnv software is the pileup algorithm. The original pileup algorithm’s I/O process is time-consuming and inefficient to read input files. Moreover, the scalability of the pileup algorithm is also poor. Therefore, we designed a new algorithm, named BamPileup, aiming to improve the performance of sequential read, and the new pileup algorithm implemented a parallel...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

Evolving-Pattern Analysis of Transient and Long-Term Biomarkers for Cancers: Hepatocellular Carcinoma as a Case
Abstract Cancer is a complex disease arises from combinations of changes that occur over a period of time. With the development of bioinformatics, more and more biomarkers representing changes in cancers had been identified using gene expression profiles. However, biomarkers alone are quite limited in explaining the molecular processes occurred in the due process. In this paper, we develop an evolving-pattern analysis pipeline for in-depth studies of gene expression changes during different disease stages, choosing hepatocellular carcinoma (HCC) as a case. Enrichment analyses were performed on three levels: funct...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

Magnetic Nanoparticles-Loaded Physarum polycephalum : Directed Growth and Particles Distribution
Abstract Slime mold Physarum polycephalum is a single cell visible by an unaided eye. The slime mold optimizes its network of protoplasmic tubes to minimize expose to repellents and maximize expose to attractants and to make efficient transportation of nutrients. These properties of P. polycephalum, together with simplicity of its handling and culturing, make it a priceless substrate for designing novel sensing, computing and actuating architectures in living amorphous biological substrate. We demonstrate that, by loading Physarum with magnetic particles and positioning it in a magnetic field, we can, in principl...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

Cross-Family Comparative Proteomic Study and Molecular Phylogeny of MAP Kinases in Plants
In this study 24 MAP kinase sequences from various plant species were selected in order to compare their conserved regions, amino acid composition, evolutionary orders and other statistical parameters. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing
Abstract Reads classification is an important fundamental problem in metagenomics study. With the development of next-generation sequencing, metagenome samples can be generated using much less money and time. However, the short reads generated by next-generation sequencing make the problem of reads classification much more difficult than before. None of the existing tools can assign NGS short reads to each genome accurately, which limit their use in real application. Fortunately, in many applications, it is meaningless to separate all the species in the metagenome sample from each other. That is because we usuall...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

A Filter Feature Selection Method Based on MFA Score and Redundancy Excluding and It’s Application to Tumor Gene Expression Data Analysis
Abstract Feature selection techniques have been widely applied to tumor gene expression data analysis in recent years. A filter feature selection method named marginal Fisher analysis score (MFA score) which is based on graph embedding has been proposed, and it has been widely used mainly because it is superior to Fisher score. Considering the heavy redundancy in gene expression data, we proposed a new filter feature selection technique in this paper. It is named MFA score+ and is based on MFA score and redundancy excluding. We applied it to an artificial dataset and eight tumor gene expression datasets to select...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 20, 2015 Category: Bioinformatics Source Type: research

Optimization of the Biosynthesis Conditions of Daptomycin by the Biostatistical Methodology
Abstract Response surface methodology (RSM) was employed to optimize medium components including oxygen vector of n-dodecane of a mutant strain GC-63 of Streptomyces roseosporus NRRL 11379. The two-level Plackett–Burman design (PB factorial design) with fourteen variables including oxygen vector was used to screen the most significant factors affecting antibiotic production. Then, the RSM based on center composite design was used to identify the optimum levels of the significant variables to generate optimal response. Glucose, soybean meal, asparagine and n-dodecane were screened to significantly influence t...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 18, 2015 Category: Bioinformatics Source Type: research

Predicting the Binding Affinity of ERβ Ligands Based on a Novel Variable Selection Method
Abstract A number of descriptors were employed to characterize the molecular structures of the 128 estrogen receptor β ligands. A quantitative structure–activity relationship (QSAR) model of these compounds was developed by the variable selection method based on variable interaction. The QSAR model with five descriptors was internally and externally validated. The determination coefficient (R 2) and the leave-one-out cross-validated correlation coefficient (Q 2) are 0.8272 and 0.8041, respectively. The estimated correlation coefficient of the external validation is 0.8255. Th...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 3, 2015 Category: Bioinformatics Source Type: research

Computational Identification of MicroRNAs and Their Targets from Finger Millet ( Eleusine coracana )
In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - October 24, 2015 Category: Bioinformatics Source Type: research

Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach
In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1–6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 b...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 15, 2015 Category: Bioinformatics Source Type: research

Comparing Performances of Multiple Comparison Methods in Commonly Used 2 ×  C Contingency Tables
This study aims at mentioning briefly multiple comparison methods such as Bonferroni, Holm–Bonferroni, Hochberg, Hommel, Marascuilo, Tukey, Benjamini–Hochberg and Gavrilov–Benjamini–Sarkar for contingency tables, through the data obtained from a medical research and examining their performances by simulation study which was constructed as the total 36 scenarios to 2 × 4 contingency table. As results of simulation, it was observed that when the sample size is more than 100, the methods which can preserve the nominal alpha level are Gavrilov–Benjamini–Sarkar, Holm–Bon...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 10, 2015 Category: Bioinformatics Source Type: research

A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on the TianHe-2 Supercomputer
Abstract ’ The de novo assembly of DNA sequences is increasingly important for biological researches in the genomic era. After more than one decade since the Human Genome Project, some challenges still exist and new solutions are being explored to improve de novo assembly of genomes. String graph assembler (SGA), based on the string graph theory, is a new method/tool developed to address the challenges. In this paper, based on an in-depth analysis of SGA we prove that the SGA-based sequence de novo assembly is an NP-complete problem. According to our analysis, SGA outperforms other similar methods/tools i...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 24, 2015 Category: Bioinformatics Source Type: research

Erratum to: Flavonoids as Multi-Target Inhibitors for Proteins Associated with Ebola Virus: In Silico Discovery Using Virtual Screening and Molecular Docking Studies
(Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - September 18, 2015 Category: Bioinformatics Source Type: research

Identification of Potential PPAR γ Agonists as Hypoglycemic Agents: Molecular Docking Approach
Abstract Peroxisome proliferator-activated receptor gamma (PPAR γ) has become an attractive molecular target for drugs that aim to treat hyperglycemia. The object of our study is to identify the required molecular descriptor and essential amino acid residues for effective PPAR γ agonistic activity. In this work, we employed Molegro Virtual Docker program in all molecular docking simulations. Accuracy of receptor-compound docking was validated on a set of 15 PPAR γ-compound complexes for which crystallographic structures were available. The reliability of the docking results was acceptable wit...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 15, 2015 Category: Bioinformatics Source Type: research

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC
Abstract Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world’s fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignmen...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 10, 2015 Category: Bioinformatics Source Type: research

Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions
In this study, a support vector machine-based predictor called AodPred was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using feature selection method. It was observed by jackknife cross-validation test that AodPred can achieve an overall accuracy of 74.79 % in identifying antioxidant proteins. As a user-friendly tool, AodPred is freely accessible at http://lin.uestc.edu.cn/server/AntioxiPred. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the ...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2015 Category: Bioinformatics Source Type: research