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https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#1
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28196958/transcription-profiling-of-bacillus-subtilis-cells-infected-with-ar9-a-giant-phage-encoding-two-multisubunit-rna-polymerases
#2
Daria Lavysh, Maria Sokolova, Marina Slashcheva, Konrad U Förstner, Konstantin Severinov
Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5' ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28168408/ssr-enriched-genetic-linkage-maps-of-bermudagrass-cynodon-dactylon%C3%A2-%C3%A3-%C3%A2-transvaalensis-and-their-comparison-with-allied-plant-genomes
#3
Sameer Khanal, Changsoo Kim, Susan A Auckland, Lisa K Rainville, Jeevan Adhikari, Brian M Schwartz, Andrew H Paterson
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents...
February 6, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28166727/whole-genome-sequencing-of-a-plasmodium-vivax-clinical-isolate-exhibits-geographical-characteristics-and-high-genetic-variation-in-china-myanmar-border-area
#4
Shen-Bo Chen, Yue Wang, Kokouvi Kassegne, Bin Xu, Hai-Mo Shen, Jun-Hu Chen
BACKGROUND: Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. RESULTS: The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28155631/a-fast-read-alignment-method-based-on-seed-and-vote-for-next-generation-sequencing
#5
Song Liu, Yi Wang, Fei Wang
BACKGROUND: The next-generation of sequencing technologies, along with the development of bioinformatics, are generating a growing number of reads every day. For the convenience of further research, these reads should be aligned to the reference genome by read alignment tools. Despite the diversity of read alignment tools, most have no comprehensive advantage in both accuracy and speed. For example, BWA has comparatively high accuracy, but its speed leaves much to be desired, becoming a bottleneck while an increasing number of reads need to be aligned every day...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28143409/improved-annotation-with-de-novo-transcriptome-assembly-in-four-social-amoeba-species
#6
Reema Singh, Hajara M Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J Barton, Pauline Schaap, Christian Cole
BACKGROUND: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale...
January 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28123117/phylogenomics-from-whole-genome-sequences-using-atram
#7
Julie M Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I Huang, Patrick G S Grady, Kayce C Bell, Quentin C B Cronk, Lawrence Mugisha, Barry R Pittendrigh, M Soledad Leonardi, David L Reed, Kevin P Johnson
Novel sequencing technologies are rapidly expanding the size of datasets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic datasets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10-30X)...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123114/split-scores-a-tool-to-quantify-phylogenetic-signal-in-genome-scale-data
#8
Elizabeth S Allman, Laura S Kubatko, John A Rhodes
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data become more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and chromosomal inversion are expected to result in changes in the underlying gene trees along a chromosome, while changes in selective pressure and mutational rates for different genomic regions may lead to shifts in the underlying mutational process. We propose the split score as a general method for quantifying support for a particular phylogenetic relationship within a genomic data set...
November 14, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#9
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#10
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28118385/rna-sequencing-reveals-biological-networks-during-table-grapevine-fujiminori-fruit-development
#11
Lingfei Shangguan, Qian Mu, Xiang Fang, Kekun Zhang, Haifeng Jia, Xiaoying Li, Yiqun Bao, Jinggui Fang
Grapevine berry development is a complex and genetically controlled process, with many morphological, biochemical and physiological changes occurring during the maturation process. Research carried out on grapevine berry development has been mainly concerned with wine grape, while barely focusing on table grape. 'Fujiminori' is an important table grapevine cultivar, which is cultivated in most provinces of China. In order to uncover the dynamic networks involved in anthocyanin biosynthesis, cell wall development, lipid metabolism and starch-sugar metabolism in 'Fujiminori' fruit, we employed RNA-sequencing (RNA-seq) and analyzed the whole transcriptome of grape berry during development at the expanding period (40 days after full bloom, 40DAF), véraison period (65DAF), and mature period (90DAF)...
2017: PloS One
https://www.readbyqxmd.com/read/28105923/mosaic-structure-of-mycobacterium-bovis-bcg-genomes-as-a-representation-of-phage-sequences-mobility
#12
Olga L Voronina, Marina S Kunda, Ekaterina I Aksenova, Andrey N Semenov, Natalia N Ryzhova, Vladimir G Lunin, Alexandr L Gintsburg
BACKGROUND: The control of genome stability is relevant for the worldwide BCG vaccine preventing the acute forms of childhood tuberculosis. BCG sub-strains whole genome comparative analysis and revealing the triggers of sub-strains transition were the purpose of our investigation. RESULTS: Whole genome sequencing of three BCG Russia seed lots (1963, 1982, 2006 years) confirmed the stability of vaccine sub-strain genome. Comparative analysis of three Mycobacteruim bovis and nine M...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#13
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28071760/origin-and-evolution-of-mir1444-genes-in-salicaceae
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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