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Advances in Bioinformatics

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https://www.readbyqxmd.com/read/28261268/an-efficient-approach-in-analysis-of-dna-base-calling-using-neural-fuzzy-model
#1
Safa A Hameed, Raed I Hamed
This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28250767/multiple-linear-regression-for-reconstruction-of-gene-regulatory-networks-in-solving-cascade-error-problems
#2
Faridah Hani Mohamed Salleh, Suhaila Zainudin, Shereena M Arif
Gene regulatory network (GRN) reconstruction is the process of identifying regulatory gene interactions from experimental data through computational analysis. One of the main reasons for the reduced performance of previous GRN methods had been inaccurate prediction of cascade motifs. Cascade error is defined as the wrong prediction of cascade motifs, where an indirect interaction is misinterpreted as a direct interaction. Despite the active research on various GRN prediction methods, the discussion on specific methods to solve problems related to cascade errors is still lacking...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28191015/combined-docking-with-classical-force-field-and-quantum-chemical-semiempirical-method-pm7
#3
A V Sulimov, D C Kutov, E V Katkova, V B Sulimov
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28127307/in-silico-analysis-of-snps-in-park2-and-pink1-genes-that-potentially-cause-autosomal-recessive-parkinson-disease
#4
Yousuf Hasan Yousuf Bakhit, Mohamed Osama Mirghani Ibrahim, Mutaz Amin, Yousra Abdelazim Mirghani, Mohamed Ahmed Salih Hassan
Introduction. Parkinson's disease (PD) is a common neurodegenerative disorder. Mutations in PINK1 are the second most common agents causing autosomal recessive, early onset PD. We aimed to identify the pathogenic SNPs in PARK2 and PINK1 using in silico prediction software and their effect on the structure, function, and regulation of the proteins. Materials and Methods. We carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27698666/in-silico-analysis-of-gene-expression-network-components-underlying-pigmentation-phenotypes-in-the-python-identified-evolutionarily-conserved-clusters-of-transcription-factor-binding-sites
#5
Kristopher J L Irizarry, Randall L Bryden
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27688753/systematic-bioinformatic-approach-for-prediction-of-linear-b-cell-epitopes-on-dengue-e-and-prm-protein
#6
Mahesha N Nadugala, Prasad H Premaratne, Charitha L Goonasekara
B-cell epitopes on the envelope (E) and premembrane (prM) proteins of dengue virus (DENV) were predicted using bioinformatics tools, BepiPred, Ellipro, and SVMTriP. Predicted epitopes, 32 and 17 for E and prM proteins, respectively, were then characterized for their level of conservations. The epitopes, EP4/E (48-55), epitope number 4 of E protein at amino acids 48-55, EP9/E (165-182), EP11/E (218-233), EP20/E (322-349), EP21/E (326-353), EP23/E (356-365), and EP25/E (380-386), showed a high intraserotype conservancy with very low pan-serotype conservancy, demonstrating a potential target as serotype specific diagnostic markers...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27667997/prediction-and-in-silico-identification-of-novel-b-cells-and-t-cells-epitopes-in-the-s1-spike-glycoprotein-of-m41-and-cr88-793-b-infectious-bronchitis-virus-serotypes-for-application-in-peptide-vaccines
#7
Faruku Bande, Siti Suri Arshad, Mohd Hair Bejo, Saeid Kadkhodaei, Abdul Rahman Omar
Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS(175-185), was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD(279-290), HPKCNFRPENI(328-338), and NETNNAGSVSDCTAGT(54-69), were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96-100% of the total M41 strains analysed...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27555868/an-optimal-seed-based-compression-algorithm-for-dna-sequences
#8
Pamela Vinitha Eric, Gopakumar Gopalakrishnan, Muralikrishnan Karunakaran
This paper proposes a seed based lossless compression algorithm to compress a DNA sequence which uses a substitution method that is similar to the LempelZiv compression scheme. The proposed method exploits the repetition structures that are inherent in DNA sequences by creating an offline dictionary which contains all such repeats along with the details of mismatches. By ensuring that only promising mismatches are allowed, the method achieves a compression ratio that is at par or better than the existing lossless DNA sequence compression algorithms...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27478437/bioinformatics-approach-for-prediction-of-functional-coding-noncoding-simple-polymorphisms-snps-indels-in-human-braf-gene
#9
Mohamed M Hassan, Shaza E Omer, Rahma M Khalf-Allah, Razaz Y Mustafa, Isra S Ali, Sofia B Mohamed
This study was carried out for Homo sapiens single variation (SNPs/Indels) in BRAF gene through coding/non-coding regions. Variants data was obtained from database of SNP even last update of November, 2015. Many bioinformatics tools were used to identify functional SNPs and indels in proteins functions, structures and expressions. Results shown, for coding polymorphisms, 111 SNPs predicted as highly damaging and six other were less. For UTRs, showed five SNPs and one indel were altered in micro RNAs binding sites (3' UTR), furthermore nil SNP or indel have functional altered in transcription factor binding sites (5' UTR)...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27413369/multiphase-simulated-annealing-based-on-boltzmann-and-bose-einstein-distribution-applied-to-protein-folding-problem
#10
Juan Frausto-Solis, Ernesto Liñán-García, Juan Paulo Sánchez-Hernández, J Javier González-Barbosa, Carlos González-Flores, Guadalupe Castilla-Valdez
A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27366148/fullssr-microsatellite-finder-and-primer-designer
#11
Sebastián Metz, Juan Manuel Cabrera, Eva Rueda, Federico Giri, Patricia Amavet
Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27340402/agent-based-deterministic-modeling-of-the-bone-marrow-homeostasis
#12
Manish Kurhekar, Umesh Deshpande
Modeling of stem cells not only describes but also predicts how a stem cell's environment can control its fate. The first stem cell populations discovered were hematopoietic stem cells (HSCs). In this paper, we present a deterministic model of bone marrow (that hosts HSCs) that is consistent with several of the qualitative biological observations. This model incorporates stem cell death (apoptosis) after a certain number of cell divisions and also demonstrates that a single HSC can potentially populate the entire bone marrow...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27313609/evaluation-of-bioinformatic-programmes-for-the-analysis-of-variants-within-splice-site-consensus-regions
#13
Rongying Tang, Debra O Prosser, Donald R Love
The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27293431/a-support-vector-machine-classification-of-thyroid-bioptic-specimens-using-maldi-msi-data
#14
Manuel Galli, Italo Zoppis, Gabriele De Sio, Clizia Chinello, Fabio Pagni, Fulvio Magni, Giancarlo Mauri
Biomarkers able to characterise and predict multifactorial diseases are still one of the most important targets for all the "omics" investigations. In this context, Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry Imaging (MALDI-MSI) has gained considerable attention in recent years, but it also led to a huge amount of complex data to be elaborated and interpreted. For this reason, computational and machine learning procedures for biomarker discovery are important tools to consider, both to reduce data dimension and to provide predictive markers for specific diseases...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27274725/expressing-redundancy-among-linear-epitope-sequence-data-based-on-residue-level-physicochemical-similarity-in-the-context-of-antigenic-cross-reaction
#15
Salvador Eugenio C Caoili
Epitope-based design of vaccines, immunotherapeutics, and immunodiagnostics is complicated by structural changes that radically alter immunological outcomes. This is obscured by expressing redundancy among linear-epitope data as fractional sequence-alignment identity, which fails to account for potentially drastic loss of binding affinity due to single-residue substitutions even where these might be considered conservative in the context of classical sequence analysis. From the perspective of immune function based on molecular recognition of epitopes, functional redundancy of epitope data (FRED) thus may be defined in a biologically more meaningful way based on residue-level physicochemical similarity in the context of antigenic cross-reaction, with functional similarity between epitopes expressed as the Shannon information entropy for differential epitope binding...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27190510/molecular-docking-and-in-silico-admet-study-reveals-acylguanidine-7a-as-a-potential-inhibitor-of-%C3%AE-secretase
#16
Chaluveelaveedu Murleedharan Nisha, Ashwini Kumar, Prateek Nair, Nityasha Gupta, Chitrangda Silakari, Timir Tripathi, Awanish Kumar
Amyloidogenic pathway in Alzheimer's disease (AD) involves breakdown of APP by β-secretase followed by γ-secretase and results in formation of amyloid beta plaque. β-secretase has been a promising target for developing novel anti-Alzheimer drugs. To test different molecules for this purpose, test ligands like acylguanidine 7a, rosiglitazone, pioglitazone, and tartaric acid were docked against our target protein β-secretase enzyme retrieved from Protein Data Bank, considering MK-8931 (phase III trial, Merck) as the positive control...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27190509/feature-selection-has-a-large-impact-on-one-class-classification-accuracy-for-micrornas-in-plants
#17
Malik Yousef, Müşerref Duygu Saçar Demirci, Waleed Khalifa, Jens Allmer
MicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently computational miRNA detection is mainly performed using machine learning and in particular two-class classification. For machine learning, the miRNAs need to be parametrized and more than 700 features have been described. Positive training examples for machine learning are readily available, but negative data is hard to come by...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27190508/ebolavirus-database-gene-and-protein-information-resource-for-ebolaviruses
#18
Rayapadi G Swetha, Sudha Ramaiah, Anand Anbarasu, Kanagaraj Sekar
Ebola Virus Disease (EVD) is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB) and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27127506/robust-feature-selection-from-microarray-data-based-on-cooperative-game-theory-and-qualitative-mutual-information
#19
Atiyeh Mortazavi, Mohammad Hossein Moattar
High dimensionality of microarray data sets may lead to low efficiency and overfitting. In this paper, a multiphase cooperative game theoretic feature selection approach is proposed for microarray data classification. In the first phase, due to high dimension of microarray data sets, the features are reduced using one of the two filter-based feature selection methods, namely, mutual information and Fisher ratio. In the second phase, Shapley index is used to evaluate the power of each feature. The main innovation of the proposed approach is to employ Qualitative Mutual Information (QMI) for this purpose...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27110241/random-versus-deterministic-descent-in-rna-energy-landscape-analysis
#20
Luke Day, Ouala Abdelhadi Ep Souki, Andreas A Albrecht, Kathleen Steinhöfel
Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time-critical component of such methods is steepest, or gradient, descent in attraction basins of local minima. We analyse the speed-up achievable by randomised descent in attraction basins in the context of large sample sets where the size has an order of magnitude in the region of ~10(6)...
2016: Advances in Bioinformatics
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