AtEnsEMBL

James, N. I.; Graham, Neil M.H.; Clements, Debbie; Schildknecht, Beatrice; May, Sean

doi:10.1007/978-1-59745-535-0_9

Cited by 3 publications

(3 citation statements)

References 4 publications

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“…Species-specific proteomic databases have also been developed, e.g. the Nottingham arabidopsis stock centre (NASC) proteomics database (21). Usually, such databases collect proteins from different sources like Swiss-Prot (22), protein information resource (PIR) (23) or protein data bank (PDB) (24) and/or predicted proteins from gene models or messenger ribonucleic acid (mRNA) datasets.…”

Section: Tools and Datamentioning

confidence: 99%

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

Bombarely

Menda

Tecle

et al. 2010

Nucleic Acids Research

251

218

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The Sol Genomics Network (SGN; http://solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. SGN is also an open source software project, continuously developing and improving a complex system for storing, integrating and analyzing data. All code and development work is publicly visible on GitHub (http://github.com). The database architecture combines SGN-specific schemas and the community-developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools. Currently, over a hundred community annotators help curate the database. SGN can be accessed at http://solgenomics.net/.

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Section: Tools and Datamentioning

confidence: 99%

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

Bombarely

Menda

Tecle

et al. 2010

Nucleic Acids Research

251

218

View full text Add to dashboard Cite

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“…ncRNA: non‐coding RNA sequences. A t E nsembl is accessible at http://atensembl.arabidopsis.info/index.html (James et al ., 2007).…”

Section: Survey Of Bioinformatics and Computer Resourcesmentioning

confidence: 99%

Markers and mapping revisited: finding your gene

et al. 2009

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SummaryThis paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science. I. Introduction BackgroundThis paper discusses advances that have been made in the field of practical gene mapping in plants since the present authors published their guide for nonspecialists, 'Markers and mapping: we are all geneticists now' (referred to here as MM1), in connection with the 2nd New Phytologist Symposium over a decade ago ( Jones et al., 1997). During this period there has been nothing short of a revolution in understanding, in technologies and in the scale of application of molecular genetics approaches to physiological and ecological problems in the plant sciences. Substantially complete and annotated sequences of the nuclear genomes of five green plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and Physcomitrella patens) are publicly available and at least as many more are well on the way to completion, including those of representative legumes (Medicago truncatula and Glycine max), major crop species (Zea mays, Solanum lycopersicum, Sorghum ...

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“…NASC now has a public version of Genespring workgroup for community use in analyzing transcriptomic data. It also has a mature integrated genome browser AtEnsEMBL ( http://atensembl.arabidopsis.info ) ( 2 ) as part of ukcrop.net , which incorporates both TAIR and MIPS genome annotations and links through it to all of the other databases and resources.…”

Section: Topicsmentioning

confidence: 99%

In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops

Chen

Harrison

2008

Genomics, Proteomics &Amp; Bioinformatics

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A workshop on “Chips, Computers and Crops” was held in Hangzhou, China during September 26–27, 2008. The main objective of the workshop was to bring together China and UK scientists from mathematics, bioinformatics and plant molecular biology communities to exchange ideas, enhance awareness of each others’ fields, explore synergisms and make recommendations on fruitful future directions in crop science. Here we describe the contributions to the workshop, and examine some conceptual issues that lie at the foundations and future of crop systems biology.

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AtEnsEMBL

Cited by 3 publications

References 4 publications

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

Markers and mapping revisited: finding your gene

In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops

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