Có 20+ tài liệu thuộc chủ đề "Next generation sequencing"
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The integrated architecture of Cruxome offers key advantages such as an interactive and user-friendly interface and the assimilation of electronic health records of the patient. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the...
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We also noticed that although a fraction of these clusters of enhancers do overlap with super-enhancers, the majority of the enhancer clusters are different from the known super-enhancers.. Early experimental studies identify enhancers by“enhancer trap”, which has established our rudimentary understand- ing of enhancers in spite of its low-throughput and time- consuming nature [10, 11]. A large number of enhancers...
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Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. ONT is...
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Low impact of different SNP panels from two building-loci pipelines on RAD-Seq. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.. https://www.earthbiogenome.org....
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Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids.. Archaea is one of the three domains of life. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was...
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A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power. Results: We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c...
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We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform ’ s impact.. Results: The number of detected variants/variant classes per individual was highly dependent on the experimental setup. 1 Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz,...
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Extensive gene rearrangements in the mitogenomes of congeneric annelid. species and insights on the evolutionary history of the genus Ophryotrocha. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3).. However, this separation was not observed in the...
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Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides.. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCN A) method was used to characterize the relationships...
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Transcriptome analysis of the uterus of hens laying eggs differing in cuticle deposition. The quantity of cuticle varies and the deposition of a good cuticle in the uterus (Shell-gland) prevents transmission of bacteria to the egg contents.. This suggests an endogenous clock in the uterus may be a component of cuticle deposition control. The images or other third party material...
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Using full chloroplast genomes of ‘ red ’ and. yellow ’ Bixa orellana (achiote) for kmer based identification and phylogenetic inference. Background: Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. There is a wide...
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interfaces and the possibility to upload custom datasets.. Full list of author information is available at the end of the article. 1): i) GMIEC-AN is used for the analysis of a minimum of two datasets. ii) GMIEC-results parses the output of GMIEC-AN, performs the automatic selection of the modules and outputs the results. iii) GMIEC-VIS, is a tool that helps...
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Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.. Conclusion: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Full list of author information is available at the...
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The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or individual. The addition of expression data adds a new dimension to this paradigm – the sampling context. While the latter spe- cies provide us with an increasing depth of knowledge in the...
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1 Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP Brazil Full list of author information is available at the end of the article. The cytogenetics characterization of the blind cavefish revealed a karyo- type comprising 2n = 50 chromosomes with 1 or 2 microBs [20]. However, no study has presented...