Abstract：
:Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequential blocks (conserved segments). Each of the sequential blocks is considerably conserved among the protein members of an EC group. Moreover, a signature includes at least three sequential blocks that are concurrently conserved, i.e. frequently observed together in sequences. In other words, a sequence signature is consisted of residues from multiple regions of the protein sequence, which echoes the observation that an enzyme catalytic site is usually constituted of residues that are largely separated in the sequence. E1DS currently contains 5421 sequence signatures that in total cover 932 4-digital EC numbers. E1DS is evaluated based on a collection of enzymes with catalytic sites annotated in Catalytic Site Atlas. When compared to the famous pattern database PROSITE, predictions based on E1DS signatures are considered more sensitive in identifying catalytic sites and the involved residues. E1DS is available at http://e1ds.ee.ncku.edu.tw/ and a mirror site can be found at http://e1ds.csbb.ntu.edu.tw/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chien TY,Chang DT,Chen CY,Weng YZ,Hsu CMdoi
10.1093/nar/gkn324subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W291-6issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn324journal_volume
36pub_type
杂志文章abstract：:A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7315
更新日期：1988-08-11 00:00:00
abstract：:Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh104
更新日期：2004-07-16 00:00:00
abstract：:Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx017
更新日期：2017-05-19 00:00:00
abstract：:DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw447
更新日期：2016-08-19 00:00:00
abstract：:We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.12.2318
更新日期：1994-06-25 00:00:00
abstract：:The pattern of preferential DNA repair of UV-induced pyrimidine dimers was studied in repair-deficient Chinese hamster ovary (CHO) cells transfected with the human excision repair gene, ERCC-1. Repair efficiency was measured in the active dihydrofolate reductase (DHFR) gene and in its flanking, non-transcribed sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7397
更新日期：1988-08-11 00:00:00
abstract：:VL30 genetic elements constitute a murine multicopy gene family that is retrovirus-like, despite the lack of sequence homology with any known retrovirus. Over one hundred copies of VL30 units are dispersed throughout the mouse genome. We report here that the mouse genome also contains 'solo' VL30 long terminal repeats...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.5.2273
更新日期：1984-03-12 00:00:00
abstract：:2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr896
更新日期：2012-03-01 00:00:00
abstract：:Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp347
更新日期：2009-07-01 00:00:00
abstract：:Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1123
更新日期：2010-03-01 00:00:00
abstract：:LINE1s occupy 17% of the human genome and are its only active autonomous mobile DNA. L1s are also responsible for genomic insertion of processed pseudogenes and >1 million non-autonomous retrotransposons (Alus and SVAs). These elements have significant effects on gene organization and expression. Despite the importanc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt512
更新日期：2013-08-01 00:00:00
abstract：:DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we des...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku642
更新日期：2014-08-01 00:00:00
abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa980
更新日期：2021-01-08 00:00:00
abstract：:Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to envi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq614
更新日期：2010-11-01 00:00:00
abstract：:The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.55
更新日期：1999-01-01 00:00:00
abstract：:Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr987
更新日期：2012-01-01 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：:Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid agg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr726
更新日期：2012-01-01 00:00:00
abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky019
更新日期：2018-04-20 00:00:00
abstract：:Constitutive expression of major histocompatibility complex class II (MHC II) antigens normally occurs in B-lymphocytes and antigen presenting cells of the monocyte/macrophage lineage. However, many malignant tumours and transformed cells express these proteins aberrantly. We demonstrate here that the MHC II DR alpha ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4881
更新日期：1992-09-25 00:00:00
abstract：:Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.8.1857
更新日期：1976-08-01 00:00:00
abstract：:The integrase (IN) protein of human immunodeficiency virus type 1 (HIV-1) catalyzes site-specific cleavage of 2 bases from the viral long terminal repeat (LTR) sequence yet it binds DNA with little DNA sequence specificity. We have previously demonstrated that the C-terminal half of IN (amino acids 154-288) possesses ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.15.3507
更新日期：1993-07-25 00:00:00
abstract：:Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.4.970
更新日期：2001-02-15 00:00:00
abstract：:DNA non-homologous end joining, the major mechanism for the repair of DNA double-strands breaks (DSB) in mammalian cells requires the DNA-dependent protein kinase (DNA-PK), a complex composed of a large catalytic subunit of 460 kDa (DNA-PKcs) and the heterodimer Ku70-Ku80 that binds to double-stranded DNA ends. Mutati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.23.4778
更新日期：2000-12-01 00:00:00
abstract：:Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl284
更新日期：2006-07-01 00:00:00
abstract：:Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1343
更新日期：2017-05-05 00:00:00
abstract：:A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.1.39
更新日期：1982-01-11 00:00:00
abstract：:The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1235
更新日期：2011-01-01 00:00:00
abstract：:FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.8.2087
更新日期：1990-04-25 00:00:00
abstract：:Symmetry considerations of the kind of structures which can be generated when dimers of histones f2al-f3 and f2a2-f2b interact lead to the following conclusions: chromatin subunits based on closed-shell structures give rise to discrete, non-interacting nucleoprotein subunits with the histones arranged at random along ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.3.405
更新日期：1975-03-01 00:00:00
