Abstract:
:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transferring the results to a floppy disk or printer. Compression and memory efficient code further enhance the size of the matrix that can be analyzed. By generating an image of the dot matrix using software, and sending this image directly to an Epson dot matrix printer, a very detailed print out may be produced. The program has a number of user selectable options which allow a great deal of control over the analysis. The program contains no computer dependent code, and thus should work on all systems that can run UCSD Pascal.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zweig SEdoi
10.1093/nar/12.1part2.767subject
Has Abstractpub_date
1984-01-11 00:00:00pages
767-76issue
1 Pt 2eissn
0305-1048issn
1362-4962journal_volume
12pub_type
杂志文章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::In neural stem cells (NSCs), the balance between stem cell maintenance and neuronal differentiation depends on cell-fate determinants such as TRIM32. Previously, we have shown that TRIM32 associates with the RNA-induced silencing complex and increases the activity of microRNAs such as Let-7a. However, the exact mechan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv138
更新日期:2015-03-11 00:00:00
abstract::ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks400
更新日期:2012-07-01 00:00:00
abstract::The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is un...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki691
更新日期:2005-07-19 00:00:00
abstract::Translesional DNA synthesis past abasic sites proceeds with the preferential incorporation of dAMP opposite the lesion and, depending on the sequence context, one or two base deletions. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of a DNA h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2385
更新日期:1998-05-15 00:00:00
abstract::We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. DNA synthesis occurred on either circular or linear plasmids coupled to the beads, but only DNA synthesis on the circular plasmid was inhibited by geminin and a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl512
更新日期:2006-07-26 00:00:00
abstract::To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for sp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm762
更新日期:2008-01-01 00:00:00
abstract::The function of arginine, cysteine and carboxylic amino acid (glutamic and aspartic) residues of sigma was studied using chemical modification by group specific reagents. Following modification of 3 arginine residues with phenylglyoxal or 3 cysteine residues with N-ethylmaleimide (NEM) sigma activity was lost. Analysi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.9.2701
更新日期:1983-05-11 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa942
更新日期:2021-01-08 00:00:00
abstract::The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq094
更新日期:2010-06-01 00:00:00
abstract::Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.21.5937
更新日期:1991-11-11 00:00:00
abstract::Murine embryonic stem (ES) cells are commonly cultured on feeder layers of primary murine embryonic fibroblasts (MEFs). Because gene targeting experiments often involve sequential selection for multiple-drug resistance in single ES cell lines, we have developed a new mouse strain which represents an economical donor f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.18.3745
更新日期:1997-09-15 00:00:00
abstract::Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt272
更新日期:2013-06-01 00:00:00
abstract::Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription star...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.20.4042
更新日期:1996-10-15 00:00:00
abstract::Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm485
更新日期:2007-01-01 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::Nucleotide excision repair (NER) mechanism is the major pathway responsible for the removal of a large variety of bulky lesions from the genome. Two different NER subpathways have been identified, i.e. the transcription-coupled and the global genome repair pathways. For DNA-damage induced by ultraviolet light both tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.23.4653
更新日期:1996-12-01 00:00:00
abstract::Members of several classes of proto-oncogenes replicate during the first third of S-phase in two human (K562 erythroleukemia and HeLa), one Chinese hamster (CHO) and eight mouse cell lines. These cell lines exhibit a variety of specialized functions characteristic of pre-B and B cells, T cells and erythroid cells. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.1.87
更新日期:1987-01-12 00:00:00
abstract::To unravel the network of transcription factors established during development it is important to understand how genes specifically expressed during embryogenesis are regulated. Oct-4 is a transcription factor whose expression is associated with an undifferentiated cell phenotype in the early mouse embryo and is downr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.6.901
更新日期:1994-03-25 00:00:00
abstract::Transcription start and termination sites were mapped in the E. coli replication origin, oriC. Outward transcription from within oriC (promoters Pori-r and Pori-l) was found to start in vivo at position 178 for Pori-l and at positions 294 and 304 for Pori-r, respectively. These transcripts were terminated after 100-15...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.6.2479
更新日期:1987-03-25 00:00:00
abstract::Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1023
更新日期:2017-01-09 00:00:00
abstract::R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq482
更新日期:2010-07-01 00:00:00
abstract::RNA-based therapeutics, i.e. the utilization of synthetic RNA molecules to alter cellular functions, have the potential to address targets which are currently out of scope for traditional drug design pipelines. This potential however hinges on the ability to selectively deliver and internalize therapeutic RNAs into ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky577
更新日期:2018-09-19 00:00:00
abstract::A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3753
更新日期:1992-07-25 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::Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm028
更新日期:2007-01-01 00:00:00
abstract::Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni072
更新日期:2005-04-28 00:00:00
abstract::The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for downloa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh023
更新日期:2004-01-01 00:00:00
abstract::Extracellular vesicles (EVs) are membranous vesicles that are released by both prokaryotic and eukaryotic cells into the extracellular microenvironment. EVs can be categorised as exosomes, ectosomes or shedding microvesicles and apoptotic bodies based on the mode of biogenesis. EVs contain biologically active cargo of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1029
更新日期:2019-01-08 00:00:00