Advances in Bioinformatics最新文献_第6页

Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions. 剪接位点共识区域内变异分析的生物信息学程序评估。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-05-24 DOI: 10.1155/2016/5614058

Rongying Tang, Debra O Prosser, Donald R Love

{"title":"Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions.","authors":"Rongying Tang, Debra O Prosser, Donald R Love","doi":"10.1155/2016/5614058","DOIUrl":"https://doi.org/10.1155/2016/5614058","url":null,"abstract":"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. Using a collection of 222 pathogenic mutations and 50 benign polymorphisms, we evaluated the sensitivity and specificity of four in silico programmes in predicting the effect of each variant on splicing. The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. The MES and ASSP programmes gave the highest performance based on Receiver Operator Curve analysis, with an optimal cut-off of score reduction of 10%. The study also showed that the sensitivity of prediction is affected by the level of conservation of individual positions, with in silico predictions for variants at positions -4 and +7 within consensus splice sites being largely uninformative. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"5614058"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/5614058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34477255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem. 基于Boltzmann和玻色-爱因斯坦分布的多相模拟退火在蛋白质折叠问题中的应用。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-06-20 DOI: 10.1155/2016/7357123

Juan Frausto-Solis, Ernesto Liñán-García, Juan Paulo Sánchez-Hernández, J Javier González-Barbosa, Carlos González-Flores, Guadalupe Castilla-Valdez

{"title":"Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem.","authors":"Juan Frausto-Solis, Ernesto Liñán-García, Juan Paulo Sánchez-Hernández, J Javier González-Barbosa, Carlos González-Flores, Guadalupe Castilla-Valdez","doi":"10.1155/2016/7357123","DOIUrl":"https://doi.org/10.1155/2016/7357123","url":null,"abstract":"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. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"7357123"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/7357123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34668396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses. 埃博拉病毒数据库:埃博拉病毒基因和蛋白质信息资源。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-04-14 DOI: 10.1155/2016/1673284

Rayapadi G Swetha, Sudha Ramaiah, Anand Anbarasu, Kanagaraj Sekar

引用次数: 4

Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction. 抗原交叉反应中基于残差级物理化学相似性的线性表位序列数据冗余表达。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-05-04 DOI: 10.1155/2016/1276594

Salvador Eugenio C Caoili

{"title":"Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction.","authors":"Salvador Eugenio C Caoili","doi":"10.1155/2016/1276594","DOIUrl":"https://doi.org/10.1155/2016/1276594","url":null,"abstract":"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. Such similarity may be estimated in terms of structural differences between an immunogen epitope and an antigen epitope with reference to an idealized binding site of high complementarity to the immunogen epitope, by analogy between protein folding and ligand-receptor binding; but this underestimates potential for cross-reactivity, suggesting that epitope-binding site complementarity is typically suboptimal as regards immunologic specificity. The apparently suboptimal complementarity may reflect a tradeoff to attain optimal immune function that favors generation of immune-system components each having potential for cross-reactivity with a variety of epitopes. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"1276594"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/1276594","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34620741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Random versus Deterministic Descent in RNA Energy Landscape Analysis. RNA能量景观分析中的随机与确定性下降。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-03-02 DOI: 10.1155/2016/9654921

Luke Day, Ouala Abdelhadi Ep Souki, Andreas A Albrecht, Kathleen Steinhöfel

{"title":"Random versus Deterministic Descent in RNA Energy Landscape Analysis.","authors":"Luke Day, Ouala Abdelhadi Ep Souki, Andreas A Albrecht, Kathleen Steinhöfel","doi":"10.1155/2016/9654921","DOIUrl":"https://doi.org/10.1155/2016/9654921","url":null,"abstract":"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). While the gain for each individual sample might be marginal, the overall run-time improvement can be significant. Moreover, for the two nongradient methods we analysed for partial energy landscapes induced by ten different RNA sequences, we obtained that the number of observed local minima is on average larger by 7.3% and 3.5%, respectively. The run-time improvement is approximately 16.6% and 6.8% on average over the ten partial energy landscapes. For the large sample size we selected for descent procedures, the coverage of local minima is very high up to energy values of the region where the samples were randomly selected from the partial energy landscapes; that is, the difference to the total set of local minima is mainly due to the upper area of the energy landscapes. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"9654921"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/9654921","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34330444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis. 基于agent的骨髓稳态确定性建模。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-06-02 DOI: 10.1155/2016/8054219

Manish Kurhekar, Umesh Deshpande

{"title":"Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis.","authors":"Manish Kurhekar, Umesh Deshpande","doi":"10.1155/2016/8054219","DOIUrl":"https://doi.org/10.1155/2016/8054219","url":null,"abstract":"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. It also demonstrates that there is a production of sufficient number of differentiated cells (RBCs, WBCs, etc.). We prove that our model of bone marrow is biologically consistent and it overcomes the biological feasibility limitations of previously reported models. The major contribution of our model is the flexibility it allows in choosing model parameters which permits several different simulations to be carried out in silico without affecting the homeostatic properties of the model. We have also performed agent-based simulation of the model of bone marrow system proposed in this paper. We have also included parameter details and the results obtained from the simulation. The program of the agent-based simulation of the proposed model is made available on a publicly accessible website. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"8054219"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/8054219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34606483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

FullSSR: Microsatellite Finder and Primer Designer. FullSSR:微卫星查找器和引物设计器。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-06-06 DOI: 10.1155/2016/6040124

Sebastián Metz, Juan Manuel Cabrera, Eva Rueda, Federico Giri, Patricia Amavet

{"title":"FullSSR: Microsatellite Finder and Primer Designer.","authors":"Sebastián Metz, Juan Manuel Cabrera, Eva Rueda, Federico Giri, Patricia Amavet","doi":"10.1155/2016/6040124","DOIUrl":"https://doi.org/10.1155/2016/6040124","url":null,"abstract":"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. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"6040124"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/6040124","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34692637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data. 基于MALDI-MSI数据的甲状腺活检标本支持向量机分类。

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-05-17 DOI: 10.1155/2016/3791214

Manuel Galli, Italo Zoppis, Gabriele De Sio, Clizia Chinello, Fabio Pagni, Fulvio Magni, Giancarlo Mauri

{"title":"A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data.","authors":"Manuel Galli, Italo Zoppis, Gabriele De Sio, Clizia Chinello, Fabio Pagni, Fulvio Magni, Giancarlo Mauri","doi":"10.1155/2016/3791214","DOIUrl":"https://doi.org/10.1155/2016/3791214","url":null,"abstract":"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. For instance, the availability of protein and genetic markers to support thyroid lesion diagnoses would impact deeply on society due to the high presence of undetermined reports (THY3) that are generally treated as malignant patients. In this paper we show how an accurate classification of thyroid bioptic specimens can be obtained through the application of a state-of-the-art machine learning approach (i.e., Support Vector Machines) on MALDI-MSI data, together with a particular wrapper feature selection algorithm (i.e., recursive feature elimination). The model is able to provide an accurate discriminatory capability using only 20 out of 144 features, resulting in an increase of the model performances, reliability, and computational efficiency. Finally, tissue areas rather than average proteomic profiles are classified, highlighting potential discriminating areas of clinical interest. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"3791214"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/3791214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34571874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

Bioinformatics Approach for Prediction of Functional Coding/Noncoding Simple Polymorphisms (SNPs/Indels) in Human BRAF Gene. 人类BRAF基因功能编码/非编码简单多态性(snp /Indels)预测的生物信息学方法

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-07-10 DOI: 10.1155/2016/2632917

Mohamed M Hassan, Shaza E Omer, Rahma M Khalf-Allah, Razaz Y Mustafa, Isra S Ali, Sofia B Mohamed

引用次数: 14

Structural Dynamics of Human Argonaute2 and Its Interaction with siRNAs Designed to Target Mutant tdp43. 人类Argonaute2的结构动力学及其与靶向突变体tdp43的sirna的相互作用

Advances in Bioinformatics Pub Date : 2016-01-01 Epub Date: 2016-03-06 DOI: 10.1155/2016/8792814

Vishwambhar Bhandare, Amutha Ramaswamy

{"title":"Structural Dynamics of Human Argonaute2 and Its Interaction with siRNAs Designed to Target Mutant tdp43.","authors":"Vishwambhar Bhandare, Amutha Ramaswamy","doi":"10.1155/2016/8792814","DOIUrl":"https://doi.org/10.1155/2016/8792814","url":null,"abstract":"The human Argonaute2 protein (Ago2) is a key player in RNA interference pathway and small RNA recognition by Ago2 is the crucial step in siRNA mediated gene silencing mechanism. The present study highlights the structural and functional dynamics of human Ago2 and the interaction mechanism of Ago2 with a set of seven siRNAs for the first time. The human Ago2 protein adopts two conformations such as \"open\" and \"close\" during the simulation of 25 ns. One of the domains named as PAZ, which is responsible for anchoring the 3'-end of siRNA guide strand, is observed as a highly flexible region. The interaction between Ago2 and siRNA, analyzed using a set of siRNAs (targeting at positions 128, 251, 341, 383, 537, 1113, and 1115 of mRNA) designed to target tdp43 mutants causing Amyotrophic Lateral Sclerosis (ALS) disease, revealed the stable and strong recognition of siRNA by the Ago2 protein during dynamics. Among the studied siRNAs, the siRNA341 is identified as a potent siRNA to recognize Ago2 and hence could be used further as a possible siRNA candidate to target the mutant tdp43 protein for the treatment of ALS patients. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2016 ","pages":"8792814"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/8792814","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34330443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20