journal
MENU ▼
Read by QxMD icon Read
search

Evolutionary Bioinformatics Online

journal
https://www.readbyqxmd.com/read/29720870/exploring-proteins-containing-amyloidogenic-regions-in-the-proteomes-of-bacteria-of-the-order-rhizobiales
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28932103/a-modified-mean-gray-wolf-optimization-approach-for-benchmark-and-biomedical-problems
#14
Narinder Singh, S B Singh
A modified variant of gray wolf optimization algorithm, namely, mean gray wolf optimization algorithm has been developed by modifying the position update (encircling behavior) equations of gray wolf optimization algorithm. The proposed variant has been tested on 23 standard benchmark well-known test functions (unimodal, multimodal, and fixed-dimension multimodal), and the performance of modified variant has been compared with particle swarm optimization and gray wolf optimization. Proposed algorithm has also been applied to the classification of 5 data sets to check feasibility of the modified variant...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28894353/optimized-next-generation-sequencing-genotype-haplotype-calling-for-genome-variability-analysis
#15
Javier Navarro, Bruno Nevado, Porfidio Hernández, Gonzalo Vera, Sebastián E Ramos-Onsins
The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to obtain a high SNP recovery and low false discovery rate but are not designed to account appropriately the frequency of the variants...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28894352/hierarchical-association-coefficient-algorithm-new-method-for-genome-wide-association-study
#16
Bongsong Kim
Hierarchical association coefficient algorithm calculates the degree of association between observations and categories into a value named hierarchical association coefficient (HA-coefficient) between 0 for the lower limit and 1 for the upper limit. The HA-coefficient algorithm can be operated with stratified ascending categories based on the average of observations in each category. The upper limit refers to a condition where observations are increasingly ordered into the stratified ascending categories, whereas the lower limit refers to a condition where observations are decreasingly ordered into the stratified ascending categories...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28890653/complete-mitochondrial-genomes-of-the-cherskii-s-sculpin-cottus-czerskii-and-siberian-taimen-hucho-taimen-reveal-genbank-entry-errors-incorrect-species-identification-and-recombinant-mitochondrial-genome
#17
Evgeniy S Balakirev, Pavel A Saveliev, Francisco J Ayala
The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28835734/embedded-based-graphics-processing-unit-cluster-platform-for-multiple-sequence-alignments
#18
Jyh-Da Wei, Hui-Jun Cheng, Chun-Yuan Lin, Jin Ye, Kuan-Yu Yeh
High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28747815/identification-of-very-small-open-reading-frames-in-the-genomes-of-holmes-jungle-virus-ord-river-virus-and-wongabel-virus-of-the-genus-hapavirus-family-rhabdoviridae
#19
REVIEW
Aneta Gubala, Susan Walsh, Jane McAllister, Richard Weir, Steven Davis, Lorna Melville, Ian Mitchell, Dieter Bulach, Penny Gauci, Alex Skvortsov, David Boyle
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28680266/genome-wide-identification-and-comparative-analysis-of-albumin-family-in-vertebrates
#20
Shugang Li, Yiping Cao, Fang Geng
Albumins are the most well-known globular proteins, and the most typical representatives are the serum albumins. However, less attention was paid to the albumin family, except for the human and bovine serum albumin. To characterize the features of albumin family, we have mined all the putative albumin proteins from the available genome sequences. The results showed that albumin is widely distributed in vertebrates, but not present in the bacteria and archaea. The phylogenetic analysis of vertebrate albumin family implied an evolutionary relationship between members of serum albumin, α-fetoprotein, vitamin D-binding protein, and afamin...
2017: Evolutionary Bioinformatics Online
journal
journal
41143
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"