Abstract：
:Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Keith JM,Cochran DA,Lala GH,Adams P,Bryant D,Mitchelson KRdoi
10.1093/nar/gnh022keywords:
subject
Has Abstractpub_date
2004-02-18 00:00:00pages
e35issue
3eissn
0305-1048issn
1362-4962pii
32/3/e35journal_volume
32pub_type
杂志文章abstract：:Mutational analysis has shown that the integrity of the region in domain III of 25S rRNA that is involved in binding of ribosomal protein L25 is essential for the production of mature 25S rRNA in the yeast Saccharomyces cerevisiae. However, even structural alterations that do not noticeably affect recognition by L25, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.24.5001
更新日期：2001-12-15 00:00:00
abstract：:We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.19.3722
更新日期：1996-10-01 00:00:00
abstract：:The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.5.1105
更新日期：1991-03-11 00:00:00
abstract：:Conventional chemotherapy remains the primary treatment option for triple-negative breast cancer (TNBC). However, the current chemotherapeutic drugs have limited effects on TNBC, and often lead to serious side effects as well as drug resistance. Thus, more effective therapeutic options are sorely needed. As c-MYC onco...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz835
更新日期：2019-11-18 00:00:00
abstract：:Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Streptococcus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs (frequent words). The character and extent of frequent words are strikingly different among these genomes. The frequent words...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf534
更新日期：2002-10-01 00:00:00
abstract：:Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of target site recognition. Cleavage specificity is typically evaluated by low throughput assays (T7 endonucleas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv137
更新日期：2015-03-31 00:00:00
abstract：:Dinucleoside diphosphates of the general type pGpN have been prepared enzymatically using ribonuclease N1. Alkylated uridines or cytidines, which are products of carcinogens acting on nucleic acids, were tested in dinucleoside diphosphates for their ability to stimulate the binding of Ala- or Val-tRNA to ribosomes. O2...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.4.1709
更新日期：1979-04-01 00:00:00
abstract：:The control of messenger RNA (mRNA) function by micro RNAs (miRNAs) in animal cells requires the GW182 protein. GW182 is recruited to the miRNA repression complex via interaction with Argonaute protein, and functions downstream to repress protein synthesis. Interaction with Argonaute is mediated by GW/WG repeats, whic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq501
更新日期：2010-10-01 00:00:00
abstract：:ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modelle...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1091
更新日期：2011-01-01 00:00:00
abstract：:Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr467
更新日期：2011-07-01 00:00:00
abstract：:NRPS-PKS is web-based software for analysing large multi-enzymatic, multi-domain megasynthases that are involved in the biosynthesis of pharmaceutically important natural products such as cyclosporin, rifamycin and erythromycin. NRPS-PKS has been developed based on a comprehensive analysis of the sequence and structur...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh359
更新日期：2004-07-01 00:00:00
abstract：:Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a subset of these proteins. SDPMOD addresses this deficit in structural information by providing a freely available automated...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh394
更新日期：2004-07-01 00:00:00
abstract：:The DNA replication, plasmid segregation and transactivation functions of Epstein-Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein-Barr virus latent origin of replication, oriP . EBNA1 molecules bound to these ele...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.19.4462
更新日期：1998-10-01 00:00:00
abstract：:Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.2.e4
更新日期：2002-01-15 00:00:00
abstract：:Multivalent cations are known to condense DNA into higher ordered structures, including toroids and rods. Here we report that solid supports treated with monovalent or multivalent cationic silanes, followed by removal of soluble molecules, can condense DNA. The mechanism of this surface-directed condensation depends o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.2.588
更新日期：1998-01-15 00:00:00
abstract：:The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks739
更新日期：2012-11-01 00:00:00
abstract：:We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh379
更新日期：2004-07-01 00:00:00
abstract：:MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1293
更新日期：2012-04-01 00:00:00
abstract：:Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for comp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki454
更新日期：2005-07-01 00:00:00
abstract：:THY Pol-2 intein, from Thermococcus hydrothermalis, belongs to the same allelic family as TLI Pol-2 (PI-TLII), Tfu Pol-2 (PI-TFUII) and TspTY Pol-3 mini-intein, all inserted at the pol-c site of archaeal DNA polymerase genes. This new intein was cloned, expressed in Escherichia coli and purified. The intein is a speci...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.21.4391
更新日期：2000-11-01 00:00:00
abstract：:Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg510
更新日期：2003-07-01 00:00:00
abstract：:The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the lin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.9.3703
更新日期：1987-05-11 00:00:00
abstract：:We examined the mechanism regulating the cellular levels of PNKP, the major kinase/phosphatase involved in the repair of oxidative DNA damage, and find that it is controlled by ATM phosphorylation and ubiquitylation-dependent proteasomal degradation. We discovered that ATM-dependent phosphorylation of PNKP at serines ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks909
更新日期：2012-12-01 00:00:00
abstract：:We have synthesized a family of double-stranded cDNAs (ds cDNAs) using as a template the family of highly purified protamine mRNAs from rainbow trout testis. Individual pure protamine cDNA components were isolated by cloning this family of protamine ds cDNAs in a plasmid vector (pMB9). Clones containing protamine sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.6.1463
更新日期：1981-03-25 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：:Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky762
更新日期：2018-11-16 00:00:00
abstract：:Clones carrying sequences expressed at altered abundance levels in dunce mutants were isolated by differentially screening a genomic library with cDNA probes representing the RNA population from dunce+ flies and the RNA population from dunce mutant flies. These mutants have an elevated cAMP content, so some isolates p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.20.8313
更新日期：1989-10-25 00:00:00
abstract：:DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm334
更新日期：2007-07-01 00:00:00
abstract：:RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities. The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. Its central leve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx966
更新日期：2018-01-04 00:00:00
abstract：:Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt547
更新日期：2013-09-01 00:00:00
