Abstract：
:With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schirmer M,Ijaz UZ,D'Amore R,Hall N,Sloan WT,Quince Cdoi
10.1093/nar/gku1341subject
Has Abstractpub_date
2015-03-31 00:00:00pages
e37issue
6eissn
0305-1048issn
1362-4962pii
gku1341journal_volume
43pub_type
杂志文章abstract：:We have previously identified a T lymphocyte protein which binds to a site within the LTR of the human immunodeficiency virus type 1 (HIV-1) and exerts an inhibitory effect on virus gene expression. The palindromic site (site B) recognized by this protein is related to the palindromic binding sites of members of the s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5429
更新日期：1992-10-25 00:00:00
abstract：:The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.10.3871
更新日期：1978-10-01 00:00:00
abstract：:Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh476
更新日期：2004-07-01 00:00:00
abstract：:Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt812
更新日期：2013-12-01 00:00:00
abstract：:Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl539
更新日期：2006-01-01 00:00:00
abstract：:The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5469
更新日期：1981-10-24 00:00:00
abstract：:Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa663
更新日期：2020-09-25 00:00:00
abstract：:NELF and DSIF act together to inhibit transcription elongation in vitro, and are implicated in causing promoter proximal pausing on the hsp70 gene in Drosophila. Here, further characterization of Drosophila NELF is provided. Drosophila NELF has four subunits similar to subunits of human NELF. The amino acid sequences ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki274
更新日期：2005-03-01 00:00:00
abstract：:Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Out...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.102
更新日期：1998-01-01 00:00:00
abstract：:Gold nanoparticle labels, combined with UV-visible optical absorption spectroscopic methods, are employed to probe the temperature-dependent solution properties of DNA triple helices. By using oligonucleotide-nanoparticle conjugates to characterize triplex denaturation, for the first time triplex to duplex melting tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh065
更新日期：2004-04-23 00:00:00
abstract：:Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, makin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp680
更新日期：2009-10-01 00:00:00
abstract：:The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introd...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky467
更新日期：2018-07-02 00:00:00
abstract：:Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn122
更新日期：2008-06-01 00:00:00
abstract：:Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl679
更新日期：2006-01-01 00:00:00
abstract：:The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.1.51
更新日期：1995-01-11 00:00:00
abstract：:While RNA structures have been extensively characterized in vitro, very few techniques exist to probe RNA structures inside cells. Here, we have exploited mechanisms of post-transcriptional regulation to synthesize fluorescence-based probes that assay RNA structures in vivo. Our probing system involves the co-expressi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1191
更新日期：2015-01-01 00:00:00
abstract：:The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1155
更新日期：2010-03-01 00:00:00
abstract：:In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.18.4344
更新日期：1993-09-11 00:00:00
abstract：:The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of se...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh039
更新日期：2004-01-01 00:00:00
abstract：:High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku370
更新日期：2014-07-01 00:00:00
abstract：:Based on parameters governing promoter activity and using regulatory elements of the lac, ara and tet operon transcription control sequences were composed which permit the regulation in Escherichia coli of several gene activities independently and quantitatively. The novel promoter PLtetO-1 allows the regulation of ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.6.1203
更新日期：1997-03-15 00:00:00
abstract：:Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3941
更新日期：1990-07-11 00:00:00
abstract：:Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.604
更新日期：2001-02-01 00:00:00
abstract：:RNA silencing is an evolutionarily conserved mechanism triggered by double-stranded RNA that is processed into 21- to 24-nt small interfering (si)RNA or micro (mi)RNA by RNaseIII-like enzymes called Dicers. Gene regulations by RNA silencing have fundamental implications in a large number of biological processes that i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku422
更新日期：2014-07-01 00:00:00
abstract：:We have used photo-crosslinking to investigate the structure and dynamics of four-way junction hairpin ribozyme constructs. Four phenylazide photo-crosslinkers were coupled to 2'-NH2-modified U+2 in the substrate and irradiated at different Mg2+ concentrations and temperatures. Consistent with the role of divalent met...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki237
更新日期：2005-02-18 00:00:00
abstract：:The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into DNA in vitro. To determine the effects of this incorporation on DNA structure and function, the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides containing dFdC were made using automated sol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1763
更新日期：1992-04-11 00:00:00
abstract：:In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq215
更新日期：2010-08-01 00:00:00
abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf107
更新日期：2002-10-15 00:00:00
abstract：:Sequences preceding the minimal promoter play a role in the differential expression of the Xenopus somatic and oocyte-type 5S RNA genes. In this report, the somatic sequences between -32 and +37 are shown to increase transcriptional activity in microinjected embryos, yet have little to no effect in microinjected oocyt...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：
更新日期：1989-11-25 00:00:00
abstract：:The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.23.4553
更新日期：1999-12-01 00:00:00
