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Evolutionary Bioinformatics Online

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https://www.readbyqxmd.com/read/30013303/modeling-cumulative-biological-phenomena-with-suppes-bayes-causal-networks
#1
Daniele Ramazzotti, Alex Graudenzi, Giulio Caravagna, Marco Antoniotti
Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wild-type conditions. Cancer and HIV are 2 common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, co-operation, and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs)...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29977111/novel-method-of-3-dimensional-graphical-representation-for-proteins-and-its-application
#2
Zhao-Hui Qi, Ke-Cheng Li, Jin-Long Ma, Yu-Hua Yao, Ling-Yun Liu
In this article, we propose a 3-dimensional graphical representation of protein sequences based on 10 physicochemical properties of 20 amino acids and the BLOSUM62 matrix. It contains evolutionary information and provides intuitive visualization. To further analyze the similarity of proteins, we extract a specific vector from the graphical representation curve. The vector is used to calculate the similarity distance between 2 protein sequences. To prove the effectiveness of our approach, we apply it to 3 real data sets...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899660/detecting-the-population-structure-and-scanning-for-signatures-of-selection-in-horses-equus-caballus-from-whole-genome-sequencing-data
#3
Cheng Zhang, Pan Ni, Hafiz Ishfaq Ahmad, M Gemingguli, A Baizilaitibei, D Gulibaheti, Yaping Fang, Haiyang Wang, Akhtar Rasool Asif, Changyi Xiao, Jianhai Chen, Yunlong Ma, Xiangdong Liu, Xiaoyong Du, Shuhong Zhao
Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899659/in-silico-study-on-molecular-sequences-for-identification-of-paphiopedilum-species
#4
Huyen-Trang Vu, Phuong Huynh, Hoang-Dung Tran, Ly Le
Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY , followed by ACO, DEF 4, and RAD 51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB - rbc L gave the highest species resolution (76...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899658/integrating-phylogenetic-and-network-approaches-to-study-gene-family-evolution-the-case-of-the-agamous-family-of-floral-genes
#5
Daniel S Carvalho, James C Schnable, Ana Maria R Almeida
The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29881251/atram-2-0-an-improved-flexible-locus-assembler-for-ngs-data
#6
REVIEW
Julie M Allen, Raphael LaFrance, Ryan A Folk, Kevin P Johnson, Robert P Guralnick
Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29844654/molecular-evolution-and-functional-divergence-of-the-iglon-family
#7
Norwin Kubick, Desiree Brösamle, Michel-Edwar Mickael
IgLON family is a subgroup of cell adhesion molecules which is known to have diverse roles in neuronal development. IgLONs are characterized by possessing 3 Ig-like C2 domains, which play a part in mediating various cellular interactions. Recently, IgLONs have been shown to be expressed at the blood-brain barrier (BBB). However, our understanding of the genetic divergence patterns and evolutionary rates of these proteins in relation to their functions, in general, and at the BBB, in particular, remains inadequate...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29720870/exploring-proteins-containing-amyloidogenic-regions-in-the-proteomes-of-bacteria-of-the-order-rhizobiales
#8
Kirill S Antonets, Sergey F Kliver, Anton A Nizhnikov
Amyloids are protein fibrils with a highly ordered spatial structure called cross-β. To date, amyloids were shown to be implicated in a wide range of biological processes, both pathogenic and functional. In bacteria, functional amyloids are involved in forming biofilms, storing toxins, overcoming the surface tension, and other functions. Rhizobiales represent an economically important group of Alphaproteobacteria , various species of which are not only capable of fixing nitrogen in the symbiosis with leguminous plants but also act as the causative agents of infectious diseases in animals and plants...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29662297/graphics-processing-unit-enhanced-genetic-algorithms-for-solving-the-temporal-dynamics-of-gene-regulatory-networks
#9
REVIEW
Raúl García-Calvo, J L Guisado, Fernando Diaz-Del-Rio, Antonio Córdoba, Francisco Jiménez-Morales
Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29568218/efficient-acceleration-of-the-pair-hmms-forward-algorithm-for-gatk-haplotypecaller-on-graphics-processing-units
#10
REVIEW
Shanshan Ren, Koen Bertels, Zaid Al-Ars
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29551886/evolution-of-synonymous-codon-usage-bias-in-west-african-and-central-african-strains-of-monkeypox-virus
#11
Sudeesh Karumathil, Nimal T Raveendran, Doss Ganesh, Sampath Kumar Ns, Rahul R Nair, Vijaya R Dirisala
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29551885/decision-tree-algorithm-generated-single-nucleotide-polymorphism-barcodes-of-rbcl-genes-for-38-brassicaceae-species-tagging
#12
Cheng-Hong Yang, Kuo-Chuan Wu, Li-Yeh Chuang, Hsueh-Wei Chang
DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29511354/swphylo-a-novel-tool-for-phylogenomic-inferences-by-comparison-of-oligonucleotide-patterns-and-integration-of-genome-based-and-gene-based-phylogenetic-trees
#13
Xiaoyu Yu, Oleg N Reva
Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29511353/a-comprehensive-study-of-de-novo-genome-assemblers-current-challenges-and-future-prospective
#14
Abdul Rafay Khan, Muhammad Tariq Pervez, Masroor Ellahi Babar, Nasir Naveed, Muhammad Shoaib
Background: Current advancements in next-generation sequencing technology have made possible to sequence whole genome but assembling a large number of short sequence reads is still a big challenge. In this article, we present the comparative study of seven assemblers, namely, ABySS, Velvet, Edena, SGA, Ray, SSAKE, and Perga, using prokaryotic and eukaryotic paired-end as well as single-end data sets from Illumina platform. Results: Results showed that in case of single-end data sets, Velvet and ABySS outperformed in all the seven assemblers with comparatively low assembling time and high genome fraction...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29472760/genetic-diversity-and-functional-analysis-of-sigma-factors-in-enterobacter-cloacae-complex-resourced-from-various-niche
#15
Farah Nazir, Muhammad Ibrahim, Ghunva Zaman, Annam Hussain, Asma Muhammad Yar, Zhu Bo
Sigma factors are bacterial transcription factors that bind the core RNA polymerase and direct transcription initiation at a specific promoter site. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions and selectively increase the transcription of those genes. Here, we attempt to identify sigma factors in 5 genomes belonging to the Enterobacter cloacae complex (Ecc), a group of gram-negative bacteria that are important nosocomial pathogens. This process includes the identification of orthologous sequences, conserved motifs, domains, families, phylogenetic profiles, and protein-protein associations of these components...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29348708/hybphylomaker-target-enrichment-data-analysis-from-raw-reads-to-species-trees
#16
Tomáš Fér, Roswitha E Schmickl
Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29308007/virus-database-and-online-inquiry-system-based-on-natural-vectors
#17
Rui Dong, Hui Zheng, Kun Tian, Shek-Chung Yau, Weiguang Mao, Wenping Yu, Changchuan Yin, Chenglong Yu, Rong Lucy He, Jie Yang, Stephen St Yau
We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29104426/popmarker-identifying-phylogenetic-markers-at-the-population-level
#18
REVIEW
Huei-Mien Ke, Chun-Ping Yu, Yu-Ching Liu, Isheng J Tsai
As phylogenomic approach becomes a common practice for constructing true bacterial phylogenies, it has become apparent that single molecular markers such as 16S ribosomal DNA often lead to misclassification of species. In this study, we present a program called Popmarker that uses the true species phylogeny and identifies a minimum set of molecular markers reflecting the bacterial evolution history and phylogenetic relationship at the resolution of populations. Popmarker ranks the proteome according to the correlation of whole species tree or subtree branch length against orthologous sequence distances...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29085238/polymorphism-of-11-y-chromosome-short-tandem-repeat-markers-among-malaysian-aborigines
#19
Sofia Sakina Mohd Yussup, Marlia Marzukhi, Badrul Munir Md-Zain, Kamaruddin Mamat, Farida Zuraina Mohd Yusof
The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29051701/mgupgma-a-fast-upgma-algorithm-with-multiple-graphics-processing-units-using-nccl
#20
REVIEW
Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan, Chuan Yi Tang
A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists...
2017: Evolutionary Bioinformatics Online
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