Abstract:
:PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Duvick J,Fu A,Muppirala U,Sabharwal M,Wilkerson MD,Lawrence CJ,Lushbough C,Brendel Vdoi
10.1093/nar/gkm1041subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D959-65issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm1041journal_volume
36pub_type
杂志文章abstract::Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2019-05-07 00:00:00
abstract::We describe the further development of a widely used package of DNA/protein sequence analysis programs (1). Important revisions have been made based on user experience, and new features, multi-user capability, and a set of large scale homology programs have been added. The programs are very user friendly, economical o...
journal_title:Nucleic acids research
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abstract::In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1996-09-01 00:00:00
abstract::The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr914
更新日期:2012-01-01 00:00:00
abstract::The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threoni...
journal_title:Nucleic acids research
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pub_type: 杂志文章
doi:10.1093/nar/16.18.8835
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abstract::Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj097
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
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更新日期:1991-03-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5199
更新日期:1991-10-11 00:00:00
abstract::Resolvase enzymes that cleave DNA four-way (Holliday) junctions are required for poxvirus replication, but clinically useful inhibitors have not been developed. Here, we report an assay for resolvase cleavage activity based on fluorescence polarization (FP) for high-throughput screening and mechanistic studies. Initia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks325
更新日期:2012-09-01 00:00:00
abstract::Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm760
更新日期:2007-01-01 00:00:00
abstract::In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr080
更新日期:2011-07-01 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::NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall. Precision ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki768
更新日期:2005-08-10 00:00:00
abstract::Alpha-1-microglobulin and bikunin are two plasma glycoproteins encoded by an alpha-1-microglobulin/bikunin precursor (AMBP) gene. The strict liver-specific expression of the AMBP gene is controlled by a potent enhancer made of six clustered boxes numbered 1-6 that have been reported to be proven or potential binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.395
更新日期:1995-02-11 00:00:00
abstract::Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1230
更新日期:2010-05-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg392
更新日期:2003-06-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2013-04-01 00:00:00
abstract::The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1994-11-11 00:00:00
abstract::The last 82 nucleotides of the 6.3 kb genomic RNA of plant turnip yellow mosaic virus (TYMV), the so-called 'tRNA-like' domain, presents functional, structural and primary sequence homologies with canonical tRNAs. In particular, one of the stem-loops resembles the TPsi(pseudouridine)-branch of tRNA, except for the pre...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1998-09-01 00:00:00
abstract::Galahad (https://galahad.esat.kuleuven.be) is a web-based application for analysis of drug effects. It provides an intuitive interface to be used by anybody interested in leveraging microarray data to gain insights into the pharmacological effects of a drug, mainly identification of candidate targets, elucidation of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2015-07-01 00:00:00
abstract::Synthetic oligonucleotides were used to introduce mutations into the lacPUV5 promoter. Four mutations were obtained at positions -13, -14, and -15, with respect to the transcriptional start site. The effects of these mutations were measured in vivo and the results are discussed with respect to the consensus sequence a...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1984-05-11 00:00:00
abstract::The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined ref...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh419
更新日期:2004-07-01 00:00:00
abstract::Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidop...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2009-06-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1985-07-25 00:00:00
abstract::Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2018-04-20 00:00:00
abstract::In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.10.4083
更新日期:1984-05-25 00:00:00