Abstract：
:While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alignment of neighboring residues when aligning two residues, thus making better use of horizontal information. By modifying existing multiple alignment algorithms to make use of horizontal information, we show that this strategy is able to consistently improve over existing algorithms on a few sets of benchmark alignments that are commonly used to measure alignment accuracy, and the average improvements in accuracy can be as much as 1-3% on protein sequence alignment and 5-10% on DNA/RNA sequence alignment. Unlike previous algorithms, consistent average improvements can be obtained across all identity levels.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lu Y,Sze SHdoi
10.1093/nar/gkn945subject
Has Abstractpub_date
2009-02-01 00:00:00pages
463-72issue
2eissn
0305-1048issn
1362-4962pii
gkn945journal_volume
37pub_type
杂志文章abstract：:DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp772
更新日期：2009-11-01 00:00:00
abstract：:Nuclei isolated from cultured mouse and rat cell lines initiated pre-rRNA chains at the correct site and with the correct nucleotide specificity (A for mouse, G for rat). Nucleic acid filter hybridization and S1 nuclease mapping were used to analyze the RNA products initiated with nucleoside (beta-S)triphosphates. Ini...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.21.8115
更新日期：1984-11-12 00:00:00
abstract：:The effect of temperature and primer concentration on oligonucleotide-primed transcription has been studied using the separated strands of a well-defined natural DNA as template. Results were similar to those obtained in the homopolymer-directed model systems. At high temperature and excess primer concentration mainly...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.2.445
更新日期：1977-02-01 00:00:00
abstract：:Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky828
更新日期：2018-10-12 00:00:00
abstract：:A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.7.2421
更新日期：1977-07-01 00:00:00
abstract：:RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr182
更新日期：2011-08-01 00:00:00
abstract：:Many nucleic acid-binding proteins and the AAA+ family form hexameric rings, but the mechanism of hexamer assembly is unclear. It is generally believed that the specificity in protein/RNA interaction relies on molecular contact through a surface charge or 3D structure matching via conformational capture or induced fit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn669
更新日期：2008-11-01 00:00:00
abstract：:Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku331
更新日期：2014-07-01 00:00:00
abstract：:The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm199
更新日期：2007-01-01 00:00:00
abstract：:A cDNA library was constructed from the mRNA of the ZR-75 oestrogen responsive human breast cancer cell line and screened for oestrogen regulated mRNA sequences. Of the recombinants isolated, 30 contained cDNA that corresponded to a single mRNA species of 2.1 kb that was induced between 10 and 15 fold by oestradiol tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.9.3773
更新日期：1987-05-11 00:00:00
abstract：:We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.16.6403
更新日期：1986-08-26 00:00:00
abstract：:Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw679
更新日期：2016-11-16 00:00:00
abstract：:The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.7.2369
更新日期：1977-07-01 00:00:00
abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4409
更新日期：1999-11-15 00:00:00
abstract：:Bacterial transcription factors often function as DNA-binding proteins that selectively activate or repress promoters, although the biochemical mechanisms vary. In most well-understood examples, activators function by either increasing the affinity of RNA polymerase (RNAP) for the target promoter, or by increasing the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1280
更新日期：2012-04-01 00:00:00
abstract：:alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.19.3873
更新日期：1996-10-01 00:00:00
abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5525
更新日期：1998-12-01 00:00:00
abstract：:Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.9.3061
更新日期：1979-07-11 00:00:00
abstract：:As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1368
更新日期：2016-04-20 00:00:00
abstract：:DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By takin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv501
更新日期：2015-07-13 00:00:00
abstract：:Analyses of secondary structures proposed for ribosomal RNA's show that, of the different kinds of base pairs directly adjoining the ends of postulated double-helical regions, only A-G with A at the 5' end significantly exceeds the number expected for a random base distribution. An A(syn)-G(trans) hydrogen-bonded base...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.8.2701
更新日期：1982-04-24 00:00:00
abstract：:Molecular mechanisms that regulate gene expression can occur either before or after transcription. The information for post-transcriptional regulation can lie within the sequence or structure of the RNA transcript and it has been proposed that G-quadruplex nucleic acid sequence motifs may regulate translation as well ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn511
更新日期：2008-11-01 00:00:00
abstract：:Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experimen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq557
更新日期：2010-11-01 00:00:00
abstract：:We have developed efficient methods for creating artificial transposons and inserting these transposons into plasmid targets in vitro, primarily for the purpose of DNA mapping and sequencing. A novel plasmid has been engineered to convert virtually any DNA sequence, or combination of sequences, into an artificial tran...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.18.3765
更新日期：1994-09-11 00:00:00
abstract：:Sas2p is a histone acetyltransferase implicated in the regulation of transcriptional silencing, and ORC is the six-subunit origin recognition complex involved in the initiation of DNA replication and the establishment of transcriptionally silent chromatin by silencers in yeast. We show here that SAS2 deletion (sas2Del...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn465
更新日期：2008-09-01 00:00:00
abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.e43
更新日期：2000-05-01 00:00:00
abstract：:This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.499
更新日期：1984-01-11 00:00:00
abstract：:Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minima...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv882
更新日期：2015-10-15 00:00:00
abstract：:A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.4.779
更新日期：1990-02-25 00:00:00
abstract：:The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the ini...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.17.3620
更新日期：1994-09-01 00:00:00
