共查询到20条相似文献,搜索用时 15 毫秒
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Rosario?Carmona Macarena?Arroyo María?José?Jiménez-Quesada Pedro?Seoane Adoración?Zafra Rafael?Larrosa Juan?de Dios?Alché M.?Gonzalo?Claros
Background
Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs.Results
An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm.Conclusion
Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.4.
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John M. Gaspar 《BMC bioinformatics》2018,19(1):536
Background
Advances in Illumina DNA sequencing technology have produced longer paired-end reads that increasingly have sequence overlaps. These reads can be merged into a single read that spans the full length of the original DNA fragment, allowing for error correction and accurate determination of read coverage. Extant merging programs utilize simplistic or unverified models for the selection of bases and quality scores for the overlapping region of merged reads.Results
We first examined the baseline quality score - error rate relationship using sequence reads derived from PhiX. In contrast to numerous published reports, we found that the quality scores produced by Illumina were not substantially inflated above the theoretical values, once the reference genome was corrected for unreported sequence variants. The PhiX reads were then used to create empirical models of sequencing errors in overlapping regions of paired-end reads, and these models were incorporated into a novel merging program, NGmerge. We demonstrate that NGmerge corrects errors and ambiguous bases better than other merging programs, and that it assigns quality scores for merged bases that accurately reflect the error rates. Our results also show that, contrary to published analyses, the sequencing errors of paired-end reads are not independent.Conclusions
We provide a free and open-source program, NGmerge, that performs better than existing read merging programs. NGmerge is available on GitHub (https://github.com/harvardinformatics/NGmerge) under the MIT License; it is written in C and supported on Linux.11.
Chao Zhao Yanan Chu Yanhong Li Chengfeng Yang Yuqing Chen Xumin Wang Bin Liu 《Biotechnology letters》2017,39(1):123-131
Objectives
To analyze the microbial diversity and gene content of a thermophilic cellulose-degrading consortium from hot springs in Xiamen, China using 454 pyrosequencing for discovering cellulolytic enzyme resources.Results
A thermophilic cellulose-degrading consortium, XM70 that was isolated from a hot spring, used sugarcane bagasse as sole carbon and energy source. DNA sequencing of the XM70 sample resulted in 349,978 reads with an average read length of 380 bases, accounting for 133,896,867 bases of sequence information. The characterization of sequencing reads and assembled contigs revealed that most microbes were derived from four phyla: Geobacillus (Firmicutes), Thermus, Bacillus, and Anoxybacillus. Twenty-eight homologous genes belonging to 15 glycoside hydrolase families were detected, including several cellulase genes. A novel hot spring metagenome-derived thermophilic cellulase was expressed and characterized.Conclusions
The application value of thermostable sugarcane bagasse-degrading enzymes is shown for production of cellulosic biofuel. The practical power of using a short-read-based metagenomic approach for harvesting novel microbial genes is also demonstrated.12.
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Amit Rai Michimi Nakamura Hiroki Takahashi Hideyuki Suzuki Kazuki Saito Mami Yamazaki 《Plant cell reports》2016,35(10):2091-2111
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Caleb F. Davis David A. Wheeler Hongmei Wang Yan Ding Shannon P. Dugan Matthew N. Bainbridge Donna M. Muzny Pulivarthi H. Rao Tsz-Kwong Man Sharon E. Plon Richard A. Gibbs Ching C. Lau 《Source code for biology and medicine》2016,11(1):8