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1.
Background
The popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencing technologies suffers from sequencing errors originating from different factors. For 16S rRNA metagenomics studies, the 454 pyrosequencing technology is one of the most frequently used platforms, but sequencing errors still lead to important data analysis issues (e.g. in clustering in taxonomic units and biodiversity estimation). Moreover, retaining a higher portion of the sequencing data by preserving as much of the read length as possible while maintaining the error rate within an acceptable range, will have important consequences at the level of taxonomic precision.Results
The new error correction algorithm proposed in this work - NoDe (Noise Detector) - is trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read. A benchmarking study with other denoising algorithms shows that NoDe can detect up to 75% more errors in a large scale mock community dataset, and this with a low computational cost compared to the second best algorithm considered in this study. The positive effect of NoDe in 16S rRNA studies was confirmed by the beneficial effect on the precision of the clustering of pyrosequencing reads in operational taxonomic units.Conclusions
NoDe was shown to be a computational efficient denoising algorithm for pyrosequencing reads, producing the lowest error rates in an extensive benchmarking study with other denoising algorithms.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0520-5) contains supplementary material, which is available to authorized users. 相似文献2.
Heather L. Blackburn Bradley Schroeder Clesson Turner Craig D. Shriver Darrell L. Ellsworth Rachel E. Ellsworth 《Current Genomics》2015,16(3):159-174
Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated
with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings
(IF)- genetic alterations associated with conditions or diseases unrelated to the patient’s present condition for which current tests are being performed- may have important clinical ramifications. The
current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed – actionable mutations, variants of unknown significance, or all IF? Policies
for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology
platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric,
and adult patients. 相似文献
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First detection of papillomaviruses and polyomaviruses in swimming pool waters: unrecognized recreational water‐related pathogens? 下载免费PDF全文
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Polyamines such as spermine can have interaction with protein. The aim of the present study was to investigate how spermine could influence the structure, thermal stability, and the activity of α-chymotrypsin. Kinetics, thermodynamics, molecular dynamics (MD), and docking simulations studies were conducted to investigate the effect of spermine on the activity and structure of α-Chymotrypsin (α-Chy) in 50 mM Tris–HCl buffer, with the pH 8, using different spectroscopic techniques as well as molecular docking and MD simulations. The stability and activity of α-Chy were increased in the presence of spermine. The results of the kinetic study showed that the activity of spermine was increased. Enzyme activation was accompanied by changes on the α-Chy conformation. Fluorescence intensity changes showed dynamic quenching during spermine binding. The fluorescence quenching of the α-Chy suggested the more polar location of Trp residues. Near-UV and Far-UV circular dichroism studies also demonstrated the transfer of Trp, Phe, and Tyr residues to a more flexible environment. The increase in the absorption of α-Chy in the presence of spermine was as a result of the formation of spermine–α-Chy complex. Molecular docking results revealed the presence of one binding site with a negative value for the Gibbs free energy of the binding of spermine to α-Chy. Docking study also revealed that van der Waals interactions and hydrogen bonds played a major role in stabilizing the complex. 相似文献
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Joshua D. Campbell Gang Liu Lingqi Luo Ji Xiao Joseph Gerrein Brenda Juan-Guardela John Tedrow Yuriy O. Alekseyev Ivana V. Yang Mick Correll Mark Geraci John Quackenbush Frank Sciurba David A. Schwartz Naftali Kaminski W. Evan Johnson Stefano Monti Avrum Spira Jennifer Beane Marc E. Lenburg 《RNA (New York, N.Y.)》2015,21(2):164-171
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High‐throughput sequencing (HTS) technologies generate millions of sequence reads from DNA/RNA molecules rapidly and cost‐effectively, enabling single investigator laboratories to address a variety of ‘omics’ questions in nonmodel organisms, fundamentally changing the way genomic approaches are used to advance biological research. One major challenge posed by HTS is the complexity and difficulty of data quality control (QC). While QC issues associated with sample isolation, library preparation and sequencing are well known and protocols for their handling are widely available, the QC of the actual sequence reads generated by HTS is often overlooked. HTS‐generated sequence reads can contain various errors, biases and artefacts whose identification and amelioration can greatly impact subsequent data analysis. However, a systematic survey on QC procedures for HTS data is still lacking. In this review, we begin by presenting standard ‘health check‐up’ QC procedures recommended for HTS data sets and establishing what ‘healthy’ HTS data look like. We next proceed by classifying errors, biases and artefacts present in HTS data into three major types of ‘pathologies’, discussing their causes and symptoms and illustrating with examples their diagnosis and impact on downstream analyses. We conclude this review by offering examples of successful ‘treatment’ protocols and recommendations on standard practices and treatment options. Notwithstanding the speed with which HTS technologies – and consequently their pathologies – change, we argue that careful QC of HTS data is an important – yet often neglected – aspect of their application in molecular ecology, and lay the groundwork for developing a HTS data QC ‘best practices’ guide. 相似文献