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Evolutionary Bioinformatics Online

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https://www.readbyqxmd.com/read/28932103/a-modified-mean-gray-wolf-optimization-approach-for-benchmark-and-biomedical-problems
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28680265/rapanet-a-web-tool-for-the-co-expression-analysis-of-brassica-rapa-genes
#8
Jiye Kim, Kyong Mi Jun, Joung Sug Kim, Songhwa Chae, Yoon-Mok Pahk, Tae-Ho Lee, Soo-In Sohn, Soo In Lee, Myung-Ho Lim, Chang-Kug Kim, Yoonkang Hur, Baek Hie Nahm, Yeon-Ki Kim
Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (r)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28659711/conservation-of-repeats-at-the-mammalian-kcnq1ot1-cdkn1c-region-suggests-a-role-in-genomic-imprinting
#9
Marcos De Donato, Tanveer Hussain, Hectorina Rodulfo, Sunday O Peters, Ikhide G Imumorin, Bolaji N Thomas
KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28607538/phylogenetic-analysis-of-nuclear-encoded-rna-maturases
#10
Sunita Malik, K C Upadhyaya, Sm Paul Khurana
Posttranscriptional processes, such as splicing, play a crucial role in gene expression and are prevalent not only in nuclear genes but also in plant mitochondria where splicing of group II introns is catalyzed by a class of proteins termed maturases. In plant mitochondria, there are 22 mitochondrial group II introns. matR, nMAT1, nMAT2, nMAT3, and nMAT4 proteins have been shown to be required for efficient splicing of several group II introns in Arabidopsis thaliana. Nuclear maturases (nMATs) are necessary for splicing of mitochondrial genes, leading to normal oxidative phosphorylation...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469382/performance-of-hidden-markov-models-in-recovering-the-standard-classification-of-glycoside-hydrolases
#11
Mariana Fonseca Rossi, Beatriz Mello, Carlos G Schrago
Glycoside hydrolases (GHs) are carbohydrate-active enzymes that assist the hydrolysis of glycoside bonds of complex sugars into carbohydrates. The current standard GH family classification is available in the CAZy database, which is based on the similarities of amino acid sequences and curated semi-automatically. However, with the exponential increase in data availability from genome sequences, automated classification methods are required for the fast annotation of coding sequences. Currently, the dbCAN database offers automatic annotations of signature domains from CAZy-defined classifications using a statistical approach, the hidden Markov models (HMMs)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469381/free-living-enterobacterium-pragia-fontium-24613-complete-genome-sequence-and-metabolic-profiling
#12
Kateřina Snopková, Karel Sedlář, Juraj Bosák, Eva Chaloupková, Ivo Sedláček, Ivo Provazník, David Šmajs
Pragia fontium is one of the few species that belongs to the group of atypical hydrogen sulfide-producing enterobacteria. Unlike other members of this closely related group, P. fontium is not associated with any known host and has been reported as a free-living bacterium. Whole genome sequencing and metabolic fingerprinting confirmed the phylogenetic position of P. fontium inside the group of atypical H2S producers. Genomic data have revealed that P. fontium 24613 has limited pathogenic potential, although there are signs of genome decay...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469380/a-new-hybrid-mgbpso-gsa-variant-for-improving-function-optimization-solution-in-search-space
#13
Narinder Singh, Sharandeep Singh, S B Singh
In this article, a newly hybrid nature-inspired approach (MGBPSO-GSA) is developed with a combination of Mean Gbest Particle Swarm Optimization (MGBPSO) and Gravitational Search Algorithm (GSA). The basic inspiration is to integrate the ability of exploitation in MGBPSO with the ability of exploration in GSA to synthesize the strength of both approaches. As a result, the presented approach has the automatic balance capability between local and global searching abilities. The performance of the hybrid approach is tested on a variety of classical functions, ie, unimodal, multimodal, and fixed-dimension multimodal functions...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469379/a-method-to-categorize-2-dimensional-patterns-using-statistics-of-spatial-organization
#14
Juan López-Sauceda, Mara D Rueda-Contreras
We developed a measurement framework of spatial organization to categorize 2-dimensional patterns from 2 multiscalar biological architectures. We propose that underlying shapes of biological entities can be approached using the statistical concept of degrees of freedom, defining it through expansion of area variability in a pattern. To help scope this suggestion, we developed a mathematical argument recognizing the deep foundations of area variability in a polygonal pattern (spatial heterogeneity). This measure uses a parameter called eutacticity...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469378/simulation-based-evaluation-of-hybridization-network-reconstruction-methods-in-the-presence-of-incomplete-lineage-sorting
#15
Olga K Kamneva, Noah A Rosenberg
Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469377/discovery-and-characterisation-of-castlerea-virus-a-new-species-of-negevirus-isolated-in-australia
#16
Caitlin A O'Brien, Breeanna J McLean, Agathe M G Colmant, Jessica J Harrison, Sonja Hall-Mendelin, Andrew F van den Hurk, Cheryl A Johansen, Daniel Watterson, Helle Bielefeldt-Ohmann, Natalee D Newton, Benjamin L Schulz, Roy A Hall, Jody Hobson-Peters
With advances in sequencing technologies, there has been an increase in the discovery of viruses that do not group with any currently described virus families. The newly described taxon Negevirus encompasses a group of viruses displaying an insect-specific phenotype which have been isolated from multiple host species on numerous continents. Using a broad-spectrum virus screening assay based on the detection of double-stranded RNA and next-generation sequencing, we have detected a novel species of negevirus, from Anopheles, Culex, and Aedes mosquitoes collected in 4 geographically separate regions of Australia...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469376/the-ds1-transposon-provides-messages-that-yield-unique-profiles-of-protein-isoforms-and-acts-synergistically-with-ds-to-enrich-proteome-complexity-via-exonization
#17
Yuh-Chyang Charng, Lung-Hsin Hsu, Li-Yu Daisy Liu
In exonization events, Ds1 may provide donor and/or acceptor sites for splicing after inserting into genes and be incorporated into new transcripts with new exon(s). In this study, the protein variants of Ds1 exonization yielding additional functional profile(s) were studied. Unlike Ds exonization, which creates new profiles mostly by incorporating flanking intron sequences with the Ds message, Ds1 exonization additionally creates new profiles through the presence or absence of Ds1 messages. The number of unique functional profiles harboring Ds1 messages is 1...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469375/numericware-i-identical-by-state-matrix-calculator
#18
REVIEW
Bongsong Kim, William D Beavis
We introduce software, Numericware i, to compute identical by state (IBS) matrix based on genotypic data. Calculating an IBS matrix with a large dataset requires large computer memory and takes lengthy processing time. Numericware i addresses these challenges with 2 algorithmic methods: multithreading and forward chopping. The multithreading allows computational routines to concurrently run on multiple central processing unit (CPU) processors. The forward chopping addresses memory limitation by dividing a dataset into appropriately sized subsets...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469374/correction-to-notes-on-the-statistical-power-of-the-binary-state-speciation-and-extinction-bisse-model
#19
Alexander Gamisch
[This corrects the article DOI: 10.4137/EBO.S39732.].
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28469373/the-use-of-next-generation-sequencing-in-the-identification-of-a-fastidious-pathogen-a-lesson-from-a-clinical-setup
#20
Amr Tm Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail, Hamsa T Tayeb
Clostridium haemolyticum is the causal agent of bacillary hemoglobinuria in cattle, goat, sheep, and ruminants. In this study, we report the first recorded human-infecting C. haemolyticum strain collected from an 18-year-old woman diagnosed with acute lymphoblastic leukemia. After failure of traditional techniques, only next-generation sequencing (NGS) technology in combination with bioinformatics, phylogenetic, and pathogenomics analyses revealed that our King Faisal Specialist Hospital and Research Center (KFSHRC) bacterial isolate belongs to C...
2017: Evolutionary Bioinformatics Online
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