Abstract:
:Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating subsequences of the chromosomes. Given this model, the determination of non-called subsequences between any gene and its nearest neighbors requires an exhaustive search of all gene calls associated with the chromosome. Further compounding the issue, the location of intergenic regions for many called genes cannot be resolved unambiguously due to uncertainties in gene boundaries, as well as the presence of other conflicting gene calls. To address these difficulties we have constructed the PACRAT (http://www.biosci.ohio-state.edu/~pacrat/) database system. PACRAT preprocesses GenBank genome submissions, evaluates for every gene the character of its relationship to those genes nearest to it, and produces a relationally linked model of the gene ordering for the genome. Using this information, the interface allows the researcher to query gene data as well as intergenic sequence data based on a number of criteria. These include the ability to filter searches based on the status of start and stop positions, or upstream/downstream sequences as conflicting with called genes and automated extension of upstream or downstream searches to find probable operon promoters or terminators. The database is also indexed by KEGG classification, allowing, for example, functionally-related groups of high-quality promoter-containing regions to be easily retrieved as a group.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ray WC,Daniels CJdoi
10.1093/nar/gkg013keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
109-13issue
1eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.3.523
更新日期:1976-03-01 00:00:00
abstract::UV-irradiation (lambda = 254 nm) of liquid aqueous solutions of deoxyguanosine in the presence of oxygen at pH less than 7 causes an intensive degradation of nucleoside. The quantum yield estimated from A254 decrease for the reaction mixture was found to be 1.5X10(-4) at doses to 150 E/mole. The rate of A254 decrease ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.4.955
更新日期:1977-04-01 00:00:00
abstract::According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw371
更新日期:2016-09-06 00:00:00
abstract::The engineering of new enzymes that efficiently and specifically modify DNA sequences is necessary for the development of enhanced gene therapies and genetic studies. To address this need, we developed a robust strategy for evolving site-specific recombinases with novel substrate specificities. In this system, recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq125
更新日期:2010-07-01 00:00:00
abstract::Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the protei...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkh315
更新日期:2004-02-27 00:00:00
abstract::RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.9.2125
更新日期:1998-05-01 00:00:00
abstract::Thyroglobulin (Tg), the precursor of thyroid hormones, is a 660.000 Da dimeric glycoprotein synthesized exclusively in the thyroid gland. We have cloned the human thyroglobulin gene from cosmid and phage libraries and constructed a complete restriction map. The gene encodes an 8.7 kb mRNA, covers at least 300 kb DNA a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.13.5171
更新日期:1986-07-11 00:00:00
abstract::Arylsulfatase, produced by Chlamydomonas reinhardtii during sulfur-limited growth, is secreted into the periplasmic space and is readily assayed using a chromogenic substrate. To assess the usefulness of the gene encoding arylsulfatase (ars) as a reporter gene in C. reinhardtii, we have fused the promoter region of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.2959
更新日期:1992-06-25 00:00:00
abstract::Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1165
更新日期:2015-01-01 00:00:00
abstract::The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1025
更新日期:2021-01-08 00:00:00
abstract::The "ovalbumin Y" gene, one of three which constitute the ovalbumin gene family in chicken has been completely sequenced. The exact location of exons can be derived from the comparison with the ovalbumin gene sequence and from the map previously established by electron microscopy analysis. During evolution of the Y ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4363
更新日期:1982-07-24 00:00:00
abstract::Conformations of 8-bromo-2'-[unk]-triisopropylbenzenesulfonyladenosine ([unk]) and its 3'-[unk]-isomer ([unk]) in solution have been determined by the use of intramolecular nuclear Overhauser effects in (1)H NMR spectroscopy. Compound [unk] has been proved to have a conformation in which the adenosine and benzene ring...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.6.823
更新日期:1974-06-01 00:00:00
abstract::Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISP...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1233
更新日期:2020-03-18 00:00:00
abstract::In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni055
更新日期:2005-03-22 00:00:00
abstract::Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1110
更新日期:2012-03-01 00:00:00
abstract::Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.405
更新日期:2002-01-01 00:00:00
abstract::Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw843
更新日期:2016-11-16 00:00:00
abstract::The final step in the maturation of paramyxoviruses, orthomyxoviruses and viruses of several other families, entails the budding of the viral nucleocapsid through the plasma membrane of the host cell. Many medically important viruses, such as influenza, parainfluenza, respiratory syncytial virus (RSV) and Ebola, can f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm246
更新日期:2007-01-01 00:00:00
abstract::Structural changes of reconstituted SV 40 minichromosomes have been studied in relation to the salt concentration and addition of histone H1 by sedimentation and electron microscopy. Sedimentation data are represented as functions of the NaCl concentration and the Debye-Hückel electrostatic screening radius 1/alpha. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.11.3581
更新日期:1979-08-10 00:00:00
abstract::The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9163
更新日期:1987-11-25 00:00:00
abstract::We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.3.1051
更新日期:1989-02-11 00:00:00
abstract::Southern blot analyses using reduced stringency hybridization conditions have been employed to search for sequence homologies between rodent VL30 genes and murine leukemia virus (MuLV) proviruses. These constitute two classes of transposon-like elements previously believed to be genetically unrelated. Our results demo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.2.305
更新日期:1983-01-25 00:00:00
abstract::The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg626
更新日期:2003-07-01 00:00:00
abstract::The effect of [Na+] on the stability and conformation of penicillium chrysogenum mycophage dsRNA (PCMdsRNA) was investigated using CD and UV optical techniques. Thermal melting profiles reveal prominent fine structure attributed to at least four regions of structural dissimilarity. A constant increased thermal stabili...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.6.759
更新日期:1975-06-01 00:00:00
abstract::The multiprotein complexes involved in active dis-ruption of chromatin structure, homologous to yeast SWI/SNF complex, have been described for human and Drosophila cells. In all SWI/SNF-class complexes characterised so far, one of the key components is the SNF5-type protein. Here we describe the isolation of a plant (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.11.2393
更新日期:1999-06-01 00:00:00
abstract::The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh448
更新日期:2004-07-01 00:00:00
abstract::The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr248
更新日期:2011-07-01 00:00:00
abstract::Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25-27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recogni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh899
更新日期:2004-10-22 00:00:00
abstract::Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1053
更新日期:2015-01-01 00:00:00
abstract::We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1933
更新日期:1991-04-25 00:00:00