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https://www.readbyqxmd.com/read/28071760/origin-and-evolution-of-mir1444-genes-in-salicaceae
#1
Meizhen Wang, Caili Li, Shanfa Lu
miR1444s are functionally significant miRNAs targeting polyphenol oxidase (PPO) genes for cleavage. MIR1444 genes were reported only in Populus trichocarpa. Through the computational analysis of 215 RNA-seq data, four whole genome sequences of Salicaceae species and deep sequencing of six P. trichocarpa small RNA libraries, we investigated the origin and evolution history of MIR1444s. A total of 23 MIR1444s were identified. Populus and Idesia species contain two MIR1444 genes, while Salix includes only one...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069632/a-few-sequence-polymorphisms-among-isolates-of-maize-bushy-stunt-phytoplasma-associate-with-organ-proliferation-symptoms-of-infected-maize-plants
#2
Zigmunds Orlovskis, Maria Cristina Canale, Mindia Haryono, João Roberto Spotti Lopes, Chih-Horng Kuo, Saskia A Hogenhout
BACKGROUND AND AIMS: Maize bushy stunt phytoplasma (MBSP) is a bacterial pathogen of maize (Zea mays L.) across Latin America. MBSP belongs to the 16SrI-B sub-group within the genus 'Candidatus Phytoplasma'. MBSP and its insect vector Dalbulus maidis (Hemiptera: Cicadellidae) are restricted to maize; both are thought to have coevolved with maize during its domestication from a teosinte-like ancestor. MBSP-infected maize plants show a diversity of symptoms. and it is likely that MBSP is under strong selection for increased virulence and insect transmission on maize hybrids that are widely grown in Brazil...
January 9, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28068919/construction-of-high-resolution-recombination-maps-in-asian-seabass
#3
Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye, Gen Hua Yue
BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28057681/ntcard-a-streaming-algorithm-for-cardinality-estimation-in-genomics-data
#4
Hamid Mohamadi, Hamza Khan, Inanc Birol
MOTIVATION: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k-mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k-mers, or even better, to build a histogram of k-mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28056804/indelseek-detection-of-complex-insertions-and-deletions-from-next-generation-sequencing-data
#5
Chun Hang Au, Anskar Y H Leung, Ava Kwong, Tsun Leung Chan, Edmond S K Ma
BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of "pileup" of each reference position across multiple alignments...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053114/feelnc-a-tool-for-long-non-coding-rna-annotation-and-its-application-to-the-dog-transcriptome
#6
Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Lætitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera, Merete Fredholm, Nadine Botherel, Peter A J Leegwater, Céline Le Béguec, Hille Fieten, Jeremy Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Thomas Derrien
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28045987/high-throughput-resequencing-of-maize-landraces-at-genomic-regions-associated-with-flowering-time
#7
Tiffany M Jamann, Shilpa Sood, Randall J Wisser, James B Holland
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions...
2017: PloS One
https://www.readbyqxmd.com/read/28043598/investigation-of-isoniazid-and-ethionamide-cross-resistance-by-whole-genome-sequencing-and-association-with-poor-treatment-outcomes-of-multidrug-resistant-tuberculosis-patients-in-south-africa
#8
L Malinga, J Brand, C Jansen van Rensburg, G Cassell, M van der Walt
OBJECTIVE/BACKGROUND: Ethionamide (ETH) and isoniazid (INH) are part of the backbone regimen used for the treatment of multidrug-resistant tuberculosis (MDR-TB). Both ETH and INH are structurally similar and are activated by ethA and katG gene products. Resistance to INH among MDR-TB patients may cause ETH to be ineffective, as both target nicotinamide adenine dinucleotide-dependent enoyl-acyl carrier protein reductase inhA protein and mutations within inhA gene may lead to their cross-resistance...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27993772/p3bsseq-parallel-processing-pipeline-software-for-automatic-analysis-of-bisulfite-sequencing-data
#9
Phuc-Loi Luu, Daniela Gerovska, Mikel Arrospide-Elgarresta, Sugoi Retegi-Carrión, Hans R Schöler, Marcos J Araúzo-Bravo
MOTIVATION: Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. RESULTS: We developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards...
October 6, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27991530/comparative-metagenomics-reveals-taxonomically-idiosyncratic-yet-functionally-congruent-communities-in-periodontitis
#10
Shareef M Dabdoub, Sukirth M Ganesan, Purnima S Kumar
The phylogenetic characteristics of microbial communities associated with periodontitis have been well studied, however, little is known about the functional endowments of this ecosystem. The present study examined 73 microbial assemblages from 25 individuals with generalized chronic periodontitis and 25 periodontally healthy individuals using whole genome shotgun sequencing. Core metabolic networks were computed from taxa and genes identified in at least 80% of individuals in each group. 50% of genes and species identified in health formed part of the core microbiome, while the disease-associated core microbiome contained 33% of genes and only 1% of taxa...
December 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27989988/novel-mutations-and-structural-deletions-in-tubb8-expanding-mutational-and-phenotypic-spectrum-of-patients-with-arrest-in-oocyte-maturation-fertilization-or-early-embryonic-development
#11
Biaobang Chen, Bin Li, Da Li, Zheng Yan, Xiaoyan Mao, Yao Xu, Jian Mu, Qiaoli Li, Li Jin, Lin He, Yanping Kuang, Qing Sang, Lei Wang
STUDY QUESTION: Are there any new type of mutations and novel phenotypes in patients with arrest in oocyte maturation, fertilization or early embryonic development having tubulin beta eight class VIII (TUBB8) mutations? SUMMARY ANSWER: We identified new types of mutations in TUBB8 associated with maturation, fertilization and developmental arrest. WHAT IS KNOWN ALREADY: We previously found heterozygous mutations and a homozygous frameshift/internal seven amino acid deletion in TUBB8 that are responsible for oocyte maturation arrest...
December 17, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27965082/analysis-of-whole-chloroplast-genomes-from-the-genera-of-the-clauseneae-the-curry-tribe-rutaceae-citrus-family
#12
Vikram S Shivakumar, Marc S Appelhans, Gabriel Johnson, Monica Carlsen, Elizabeth A Zimmer
The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied. Due to the recent significant taxonomic changes made to this tribe, a closer inspection of the genetic relationships among its genera has been warranted. Whole genome skimming was used to generate chloroplast genomes from six species, representing each of the four genera (Bergera, Clausena, Glycosmis, Micromelum) in the Clauseneae tribe plus one closely related outgroup (Merrillia), using the published plastome sequence of Citrus sinensis as a reference...
December 11, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27964746/alternate-locus-aware-variant-calling-in-whole-genome-sequencing
#13
Marten Jäger, Max Schubach, Tomasz Zemojtel, Knut Reinert, Deanna M Church, Peter N Robinson
BACKGROUND: The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. The new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS). METHODS: We developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#14
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27903645/upgrading-short-read-animal-genome-assemblies-to-chromosome-level-using-comparative-genomics-and-a-universal-probe-set
#15
Joana Damas, Rebecca O'Connor, Marta Farré, Vasileios Panagiotis E Lenis, Henry J Martell, Anjali Mandawala, Katie Fowler, Sunitha Joseph, Martin T Swain, Darren K Griffin, Denis M Larkin
Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes. Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27902382/genetic-diversity-and-phenotypic-associations-of-feline-caliciviruses-from-cats-in-switzerland
#16
Andrea M Spiri, Julien Thézé, Marina L Meli, Valentino Cattori, Alice Berger, Adolf Steinrigl, Oliver G Pybus, Regina Hofmann-Lehmann, Barbara Willi
Feline calicivirus (FCV) is a common viral pathogen in domestic cats worldwide. The variable regions of the capsid (VP1) gene of FCV have one of the highest recorded rates of molecular evolution. Understanding the genetic diversity and phylogeny of FCV is a prerequisite to exploring the epidemiology and pathogenesis of this virus and to the development of efficacious vaccine strategies. In this study, we undertook a nationwide molecular characterization of FCV using for the first time nearly complete capsid (VP1) gene sequences...
December 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27895624/visualizing-evolutionary-relationships-of-multidomain-proteins-an-example-from-receiver-rec-domains-of-sensor-histidine-kinases-in-the-candidatus-maribeggiatoa-str-orange-guaymas-draft-genome
#17
Barbara J MacGregor
For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27889124/assessing-genomic-prediction-accuracy-for-holstein-sires-using-bootstrap-aggregation-sampling-and-leave-one-out-cross-validation
#18
Ashley A Mikshowsky, Daniel Gianola, Kent A Weigel
Since the introduction of genome-enabled prediction for dairy cattle in 2009, genomic selection has markedly changed many aspects of the dairy genetics industry and enhanced the rate of response to selection for most economically important traits. Young dairy bulls are genotyped to obtain their genomic predicted transmitting ability (GPTA) and reliability (REL) values. These GPTA are a main factor in most purchasing, marketing, and culling decisions until bulls reach 5 yr of age and their milk-recorded offspring become available...
January 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/27882129/whole-genome-resequencing-of-100-healthy-individuals-using-dna-pooling
#19
Xiaobin Wang, Weiguo Sui, Weiqing Wu, Xianliang Hou, Minglin Ou, Yueying Xiang, Yong Dai
With the advent of next-generation sequencing technology, the cost of sequencing has significantly decreased. However, sequencing costs remain high for large-scale studies. In the present study, DNA pooling was applied as a cost-effective strategy for sequencing. The sequencing results for 100 healthy individuals obtained via whole-genome resequencing and using DNA pooling are presented in the present study. In order to minimise the likelihood of systematic bias in sampling, paired-end libraries with an insert size of 500 bp were prepared for all samples and then subjected to whole-genome sequencing using four lanes for each library and resulting in at least a 30-fold haploid coverage for each sample...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27855631/a-core-phylogeny-of-dictyostelia-inferred-from-genomes-representative-of-the-eight-major-and-minor-taxonomic-divisions-of-the-group
#20
Reema Singh, Christina Schilde, Pauline Schaap
BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa...
November 17, 2016: BMC Evolutionary Biology
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