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Evolutionary Bioinformatics Online

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https://www.readbyqxmd.com/read/28607538/phylogenetic-analysis-of-nuclear-encoded-rna-maturases
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28096646/commensal-viruses-of-mosquitoes-host-restriction-transmission-and-interaction-with-arboviral-pathogens
#12
REVIEW
Roy A Hall, Helle Bielefeldt-Ohmann, Breeanna J McLean, Caitlin A O'Brien, Agathe M G Colmant, Thisun B H Piyasena, Jessica J Harrison, Natalee D Newton, Ross T Barnard, Natalie A Prow, Joshua M Deerain, Marcus G K Y Mah, Jody Hobson-Peters
Recent advances in virus detection strategies and deep sequencing technologies have enabled the identification of a multitude of new viruses that persistently infect mosquitoes but do not infect vertebrates. These are usually referred to as insect-specific viruses (ISVs). These novel viruses have generated considerable interest in their modes of transmission, persistence in mosquito populations, the mechanisms that restrict their host range to mosquitoes, and their interactions with pathogens transmissible by the same mosquito...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28008220/prefiltering-model-for-homology-detection-algorithms-on-gpu
#13
Germán Retamosa, Luis de Pedro, Ivan González, Javier Tamames
Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27980385/current-bacterial-gene-encoding-capsule-biosynthesis-protein-capi-contains-nucleotides-derived-from-exonization
#14
Yong Wang, Xia-Fang Tao, Zhi-Xi Su, A-Ke Liu, Tian-Lei Liu, Ling Sun, Qin Yao, Ke-Ping Chen, Xun Gu
Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27980384/support-vector-machines-trained-with-evolutionary-algorithms-employing-kernel-adatron-for-large-scale-classification-of-protein-structures
#15
Nancy Arana-Daniel, Alberto A Gallegos, Carlos López-Franco, Alma Y Alanís, Jacob Morales, Adriana López-Franco
With the increasing power of computers, the amount of data that can be processed in small periods of time has grown exponentially, as has the importance of classifying large-scale data efficiently. Support vector machines have shown good results classifying large amounts of high-dimensional data, such as data generated by protein structure prediction, spam recognition, medical diagnosis, optical character recognition and text classification, etc. Most state of the art approaches for large-scale learning use traditional optimization methods, such as quadratic programming or gradient descent, which makes the use of evolutionary algorithms for training support vector machines an area to be explored...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27920488/evalmsa-a-program-to-evaluate-multiple-sequence-alignments-and-detect-outliers
#16
Alvaro Chiner-Oms, Fernando González-Candelas
We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27840574/a-comparative-in-silico-study-of-the-antioxidant-defense-gene-repertoire-of-distinct-lifestyle-trypanosomatid-species
#17
Ingrid Thaís Beltrame-Botelho, Carlos Talavera-López, Björn Andersson, Edmundo Carlos Grisard, Patricia Hermes Stoco
Kinetoplastids are an ancestral group of protists that contains free-living species and parasites with distinct mechanisms in response to stress. Here, we compared genes involved in antioxidant defense (AD), proposing an evolution model among trypanosomatids. All genes were identified in Bodo saltans, suggesting that AD mechanisms have evolved prior to adaptation for parasitic lifestyles. While most of the monoxenous and dixenous parasites revealed minor differences from B. saltans, the endosymbiont-bearing species have an increased number of genes...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27840573/a-multilayered-screening-method-for-the-identification-of-regulatory-genes-in-rice-by-agronomic-traits
#18
Young-Joo Seol, So Youn Won, Younhee Shin, Jong-Yeol Lee, Jong-Sik Chun, Yong-Kab Kim, Chang-Kug Kim
We developed a multilayered screening method that integrates both genome and transcriptome data to effectively identify regulatory genes in rice (Oryza sativa). We tested our method using eight rice accessions that differed in three important nutritional and agricultural traits, anthocyanin biosynthesis, amylose content, and heading date. In the genome resequencing of eight rice accessions with 24 RNA sequencing experiments, 98% of the preprocessed reads could be uniquely mapped to the reference genome, resulting in the identification of 42,699 unique transcripts...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27812277/a-bioinformatics-approach-for-detecting-repetitive-nested-motifs-using-pattern-matching
#19
José R Romero, Jessica A Carballido, Ingrid Garbus, Viviana C Echenique, Ignacio Ponzoni
The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27812276/ibbomsa-an-improved-biogeography-based-approach-for-multiple-sequence-alignment
#20
Rohit Kumar Yadav, Haider Banka
In bioinformatics, multiple sequence alignment (MSA) is an NP-hard problem. Hence, nature-inspired techniques can better approximate the solution. In the current study, a novel biogeography-based optimization (NBBO) is proposed to solve an MSA problem. The biogeography-based optimization (BBO) is a new paradigm for optimization. But, there exists some deficiencies in solving complicated problems such as low population diversity and slow convergence rate. NBBO is an enhanced version of BBO, in which, a new migration operation is proposed to overcome the limitations of BBO...
2016: Evolutionary Bioinformatics Online
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