- Email: [email protected]
Plant biotechnology web alert
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Genome studies and molecular genetics/Plant biotechnology Web alert Robyn M Perrin* and Philip A Wigge† A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology.
associated tools. Information about how to access these services is given on this web site.
Addresses *MSU-DOE Plant Research Laboratory, Room 110, Plant Biology Building, Michigan State University, East Lansing, Michigan 48824, USA; e-mail: [email protected] † Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; e-mail: [email protected]
Nature: A Celebration of Plant Science http://www.nature.com/nature/fow/001214.html This web site is Nature’s ‘Feature of the Week’ for December 14 2000, which describes the completion of the Arabidopsis genome sequencing project. The site includes free full-text access to some landmark Arabidopsis research articles, although not all articles are available to non-subscribers.
Current Opinion in Plant Biology 2001, 4:101-102
Celebrating the completion of the Arabidopsis genome sequencing project: a toolbox of essential Arabidopsis web sites The Arabidopsis Information Resource (TAIR) http://www.arabidopsis.org/home.html The recently redesigned TAIR web site should be the first stop for anyone working on Arabidopsis. Tools are available for BLAST, FASTA, and pattern-match searches of the Arabidopsis genome. A map viewer allows the user to view the Arabidopsis genome in terms of sequence, genetic or physical maps. Alternatively, users can locate a mapped reference sequence of their choice. If desired, portions of the Arabidopsis database can be downloaded from the TAIR using the file transfer protocol (FTP) and, hence, analyses can be performed locally. This site also maintains a collection of links to other Arabidopsis resources. The TIGR Arabidopsis thaliana Database http://www.tigr.org/tdb/ath1/htmls/index.html and http://www.tigr.org/tdb/at/alignTC.html The first web site is the Arabidopsis thaliana database maintained by The Institute of Genomic Research (TIGR), which is a member of the Arabidopsis Genome Initiative. Currently, TIGR is working on a complete Arabidopsis annotation database called ATH1. Though not yet complete, the database will ultimately contain every sequence derived from AGI sequencing projects annotated to a uniform standard. The second web site provides access to the Tentative Consensus (TC) sequences database. MIPS Arabidopsis thaliana Group http://websvr.mips.biochem.mpg.de/proj/thal/ This is the web site for the Munich Information Center for Protein Sequences (MIPS) Arabidopsis thaliana group. This group, a member of the Arabidopsis Genome Initiative, has handled data management, annotation, and analysis during the sequencing of the Arabidopsis genome. Central to the site is the MIPS Arabidopsis thaliana Database (MATDB), a database of annotated Arabidopsis sequences. Other tools, including a graphical illustration of redundancy within the Arabidopsis genome, are also available. Be sure to check out other features offered by MIPS such as PEDANT (the Protein Extraction, Description, and Analysis Tool). Arabidopsis Functional Genomics Consortium (AFGC) http://afgc.stanford.edu/ The AFGC is dedicated to providing information about Arabidopsis gene expression and function through the use of microarrays and a gene knockout facility, and to developing
Arabidopsis Newsgroup http://www.bio.net/hypermail/arab-gen/current/ and http://www.bio.net//hypermail/ARABIDOPSIS/ Arabidopsis researchers are a lively bunch. These web sites are the venue for a newsgroup, arab-gen/bionet.genome.arabidopsis, devoted entirely to communication about all things Arabidopsis. All messages posted on the site are archived and searchable. You can post a message yourself via e-mail. The Multinational Coordinated Arabidopsis 2010 Project http://www.arabidopsis.org/workshop1.html It took only ten years for the genome of Arabidopsis to be sequenced. So what’s next? This web site describes Project 2010, a coordinated international effort to elucidate the function of all Arabidopsis genes within their cellular, organismal and evolutionary context. Lehle Seeds – Arabidopsis Research Supplies http://www.arabidopsis.com/ A major commercial source for Arabidopsis research supplies operated by Lehle Seeds. However, it goes far beyond a typical commercial web site. Features include regular news updates about Arabidopsis research, descriptions of recently granted plant patents, forums for communicating about particular Arabidopsisrelated topics, teaching resources, links to software tools, and more. Of course, the Lehle Seeds catalog is also available. AIMS: Arabidopsis information Management System http://aims.cps.msu.edu/aims/ This is the web site for the Arabidopsis Information Management System (AIMS). Orders for seeds and other Arabidopsis tools from the Arabidopsis Biological Research Center (ABRC) or the Nottingham Arabidopsis Stock Centre (NASC) may be made through AIMS.
Genome studies and bioinformatics UK CropNet http://ukcrop.net/ The UK Crop Plant Bioinformatics Network (UK CropNet) maintains this site. It contains a collection of plant sequence databases and analytical software for the development, management, and distribution of plant genome information. Databases include the Arabidopsis Genome Resource (AGR), BarleyDB, BrassicaDB, forage grasses (FoggDB) and millet (MilletDB). A variety of other databases that are maintained by Cornell University, such as AlfaGenes, BeanGenes, CottonDB, and others (including one
102
entitled CoolGenes), are also mirrored on this site. All of the databases may be accessed via the Web using either the WebAce or AceBrowser interface. The UK CropNet databases were created using the ACEDB database system. If desired, users may download the databases and perform their analyses locally using ACEDB software. A variety of other software tools is also available. MOTIF: Bioinformatics Resources http://dna.Stanford.EDU/motif/ This site contains an extensive, though not comprehensive, list of bioinformatics links. It is maintained by the Brutlag Bioinformatics Group, which is located in the Biochemistry Department of Stanford University. Plant Genome Data and Information Center http://www.nal.usda.gov/pgdic/ This is the web site for the Plant Genome Data and Information Center, hosted by the National Agricultural Library and the US Department of Agriculture-Agricultural Research Service. It contains a variety of publications and links to literature and experimental resources. Although the main page appears to have been updated recently, be aware that not all of the features are supported by regular updates. ARS Genome Database Resource http://ars-genome.cornell.edu/ The US Agricultural Research Service (ARS) Genome Research Database is part of an effort “dedicated to the world’s harvest and its enhancement through crop genomics research”. This web site allows access to a variety of genome databases for crop plants. Newsletters about crop plant research and conference announcements are also available. International Organization for Plant Information http://iopi.csu.edu.au/iopi/ The International Organization for Plant Information hosts this site. Their stated goal is to “manage a series of cooperative international projects that aim to create databases of plant taxonomic information.” Several projects and resources for botanical information are available, including a Database of Plant Databases that describes plant collection efforts occurring all over the world.
Biotechnology Biotechnology: An Information Resource http://www.nal.usda.gov/bic/ This site hosts an annotated collection of biotechnology links. Regularly updated, it includes links to everything from resources on the regulations relating to genetically modified organisms to articles in the popular press about agricultural biotechnology. National Agricultural Biotechnology Council http://www.cals.cornell.edu/extension/nabc/ The National Agricultural Biotechnology Council (NABC) is a nonprofit consortium of over 30 agricultural research and teaching universities. This consortium hosts annual public meetings about “the safe, ethical, and efficacious development of agricultural biotechnology” and publishes reports and occasional papers on this subject. AgBiotechNet http://www.agbiotechnet.com/ AgBiotechNet is an online information service for agricultural biotechnology. Regularly updated, this site provides news
reports on a variety of agricultural biotechnology topics, abstracts of articles published recently in the scientific literature, conference announcements, reviews on agbiotech topics, a jobs listing, and reports. An extensive collection of agricultural biotechnology links is maintained. Full access to all features requires an individual or institutional subscription, but trial subscriptions may be obtained free of charge. Information Systems for Biotechnology http://www.nbiap.vt.edu/ This is the official web site of Information Systems for Biotechnology (ISB). The site provides information resources for agricultural biotechnology, including regular news reports, databases of US and international field testing of genetically modified organisms (GMOs), listings of US and international commercialized crops, and links to a large collection of agricultural biotechnology web sites. Intellectual Property Network http://www.delphion.com/ The Intellectual Property Network web site allows free access to a variety of patent and data collections including US patents, European patents and patent applications, patent abstracts from Japan, Patent Cooperation Treaty (PCT) applications to the World Intellectual Property Office, and others. Patent collections may be searched by keyword, patent number, boolean text, or advanced text. Users may also browse by subject. National Plant Germplasm System http://www.ars-grin.gov/npgs/ The National Plant Germplasm System (NPGS) web site seeks to provide scientists with information about germplasm collections. The NPGS is a cooperative effort by public and private organizations to collect and curate collections of crop germplasm. Users may search the germplasm collections for samples with desired features, such as a particular growth habit or resistance to a particular disease. Small germplasm samples may be requested for research purposes. Transgenic crops: An Introduction and Resource Guide http://www.colostate.edu/programs/lifesciences/TransgenicCrops/ This site provides perspective and balance to the public debate and concerns over genetically modified plants. Set up by crop scientists from the University of Colorado, the site contains a wealth of information for students and the public about virusresistant papaya, Bt corn and many other genetically modified crops. Highlights include a lively animation that provides instructions on how to make a transgenic plant as well as a discussion of the risks and concerns posed by this technology. A host on links is provided to related pages, including those of groups opposed to genetic engineering. Bioengineering Action Network of North America http://www.tao.ca/~ban/ Just in case you thought the furor over genetically modified plants was beginning to cool, you may want to visit the web site of the Bioengineering Activist Network. This group advocates the destruction of transgenic plants and associated research materials in commercial, private, public, and academic settings. The web site provides regular updates on anti-biotech demonstrations and property-destruction actions. Detailed instructions are given on how to destroy genetically modified crops.
Genome studies and molecular genetics/Plant biotechnology Web alert Robyn M Perrin* and Philip A Wigge† A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology.
associated tools. Information about how to access these services is given on this web site.
Addresses *MSU-DOE Plant Research Laboratory, Room 110, Plant Biology Building, Michigan State University, East Lansing, Michigan 48824, USA; e-mail: [email protected] † Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; e-mail: [email protected]
Nature: A Celebration of Plant Science http://www.nature.com/nature/fow/001214.html This web site is Nature’s ‘Feature of the Week’ for December 14 2000, which describes the completion of the Arabidopsis genome sequencing project. The site includes free full-text access to some landmark Arabidopsis research articles, although not all articles are available to non-subscribers.
Current Opinion in Plant Biology 2001, 4:101-102
Celebrating the completion of the Arabidopsis genome sequencing project: a toolbox of essential Arabidopsis web sites The Arabidopsis Information Resource (TAIR) http://www.arabidopsis.org/home.html The recently redesigned TAIR web site should be the first stop for anyone working on Arabidopsis. Tools are available for BLAST, FASTA, and pattern-match searches of the Arabidopsis genome. A map viewer allows the user to view the Arabidopsis genome in terms of sequence, genetic or physical maps. Alternatively, users can locate a mapped reference sequence of their choice. If desired, portions of the Arabidopsis database can be downloaded from the TAIR using the file transfer protocol (FTP) and, hence, analyses can be performed locally. This site also maintains a collection of links to other Arabidopsis resources. The TIGR Arabidopsis thaliana Database http://www.tigr.org/tdb/ath1/htmls/index.html and http://www.tigr.org/tdb/at/alignTC.html The first web site is the Arabidopsis thaliana database maintained by The Institute of Genomic Research (TIGR), which is a member of the Arabidopsis Genome Initiative. Currently, TIGR is working on a complete Arabidopsis annotation database called ATH1. Though not yet complete, the database will ultimately contain every sequence derived from AGI sequencing projects annotated to a uniform standard. The second web site provides access to the Tentative Consensus (TC) sequences database. MIPS Arabidopsis thaliana Group http://websvr.mips.biochem.mpg.de/proj/thal/ This is the web site for the Munich Information Center for Protein Sequences (MIPS) Arabidopsis thaliana group. This group, a member of the Arabidopsis Genome Initiative, has handled data management, annotation, and analysis during the sequencing of the Arabidopsis genome. Central to the site is the MIPS Arabidopsis thaliana Database (MATDB), a database of annotated Arabidopsis sequences. Other tools, including a graphical illustration of redundancy within the Arabidopsis genome, are also available. Be sure to check out other features offered by MIPS such as PEDANT (the Protein Extraction, Description, and Analysis Tool). Arabidopsis Functional Genomics Consortium (AFGC) http://afgc.stanford.edu/ The AFGC is dedicated to providing information about Arabidopsis gene expression and function through the use of microarrays and a gene knockout facility, and to developing
Arabidopsis Newsgroup http://www.bio.net/hypermail/arab-gen/current/ and http://www.bio.net//hypermail/ARABIDOPSIS/ Arabidopsis researchers are a lively bunch. These web sites are the venue for a newsgroup, arab-gen/bionet.genome.arabidopsis, devoted entirely to communication about all things Arabidopsis. All messages posted on the site are archived and searchable. You can post a message yourself via e-mail. The Multinational Coordinated Arabidopsis 2010 Project http://www.arabidopsis.org/workshop1.html It took only ten years for the genome of Arabidopsis to be sequenced. So what’s next? This web site describes Project 2010, a coordinated international effort to elucidate the function of all Arabidopsis genes within their cellular, organismal and evolutionary context. Lehle Seeds – Arabidopsis Research Supplies http://www.arabidopsis.com/ A major commercial source for Arabidopsis research supplies operated by Lehle Seeds. However, it goes far beyond a typical commercial web site. Features include regular news updates about Arabidopsis research, descriptions of recently granted plant patents, forums for communicating about particular Arabidopsisrelated topics, teaching resources, links to software tools, and more. Of course, the Lehle Seeds catalog is also available. AIMS: Arabidopsis information Management System http://aims.cps.msu.edu/aims/ This is the web site for the Arabidopsis Information Management System (AIMS). Orders for seeds and other Arabidopsis tools from the Arabidopsis Biological Research Center (ABRC) or the Nottingham Arabidopsis Stock Centre (NASC) may be made through AIMS.
Genome studies and bioinformatics UK CropNet http://ukcrop.net/ The UK Crop Plant Bioinformatics Network (UK CropNet) maintains this site. It contains a collection of plant sequence databases and analytical software for the development, management, and distribution of plant genome information. Databases include the Arabidopsis Genome Resource (AGR), BarleyDB, BrassicaDB, forage grasses (FoggDB) and millet (MilletDB). A variety of other databases that are maintained by Cornell University, such as AlfaGenes, BeanGenes, CottonDB, and others (including one
102
entitled CoolGenes), are also mirrored on this site. All of the databases may be accessed via the Web using either the WebAce or AceBrowser interface. The UK CropNet databases were created using the ACEDB database system. If desired, users may download the databases and perform their analyses locally using ACEDB software. A variety of other software tools is also available. MOTIF: Bioinformatics Resources http://dna.Stanford.EDU/motif/ This site contains an extensive, though not comprehensive, list of bioinformatics links. It is maintained by the Brutlag Bioinformatics Group, which is located in the Biochemistry Department of Stanford University. Plant Genome Data and Information Center http://www.nal.usda.gov/pgdic/ This is the web site for the Plant Genome Data and Information Center, hosted by the National Agricultural Library and the US Department of Agriculture-Agricultural Research Service. It contains a variety of publications and links to literature and experimental resources. Although the main page appears to have been updated recently, be aware that not all of the features are supported by regular updates. ARS Genome Database Resource http://ars-genome.cornell.edu/ The US Agricultural Research Service (ARS) Genome Research Database is part of an effort “dedicated to the world’s harvest and its enhancement through crop genomics research”. This web site allows access to a variety of genome databases for crop plants. Newsletters about crop plant research and conference announcements are also available. International Organization for Plant Information http://iopi.csu.edu.au/iopi/ The International Organization for Plant Information hosts this site. Their stated goal is to “manage a series of cooperative international projects that aim to create databases of plant taxonomic information.” Several projects and resources for botanical information are available, including a Database of Plant Databases that describes plant collection efforts occurring all over the world.
Biotechnology Biotechnology: An Information Resource http://www.nal.usda.gov/bic/ This site hosts an annotated collection of biotechnology links. Regularly updated, it includes links to everything from resources on the regulations relating to genetically modified organisms to articles in the popular press about agricultural biotechnology. National Agricultural Biotechnology Council http://www.cals.cornell.edu/extension/nabc/ The National Agricultural Biotechnology Council (NABC) is a nonprofit consortium of over 30 agricultural research and teaching universities. This consortium hosts annual public meetings about “the safe, ethical, and efficacious development of agricultural biotechnology” and publishes reports and occasional papers on this subject. AgBiotechNet http://www.agbiotechnet.com/ AgBiotechNet is an online information service for agricultural biotechnology. Regularly updated, this site provides news
reports on a variety of agricultural biotechnology topics, abstracts of articles published recently in the scientific literature, conference announcements, reviews on agbiotech topics, a jobs listing, and reports. An extensive collection of agricultural biotechnology links is maintained. Full access to all features requires an individual or institutional subscription, but trial subscriptions may be obtained free of charge. Information Systems for Biotechnology http://www.nbiap.vt.edu/ This is the official web site of Information Systems for Biotechnology (ISB). The site provides information resources for agricultural biotechnology, including regular news reports, databases of US and international field testing of genetically modified organisms (GMOs), listings of US and international commercialized crops, and links to a large collection of agricultural biotechnology web sites. Intellectual Property Network http://www.delphion.com/ The Intellectual Property Network web site allows free access to a variety of patent and data collections including US patents, European patents and patent applications, patent abstracts from Japan, Patent Cooperation Treaty (PCT) applications to the World Intellectual Property Office, and others. Patent collections may be searched by keyword, patent number, boolean text, or advanced text. Users may also browse by subject. National Plant Germplasm System http://www.ars-grin.gov/npgs/ The National Plant Germplasm System (NPGS) web site seeks to provide scientists with information about germplasm collections. The NPGS is a cooperative effort by public and private organizations to collect and curate collections of crop germplasm. Users may search the germplasm collections for samples with desired features, such as a particular growth habit or resistance to a particular disease. Small germplasm samples may be requested for research purposes. Transgenic crops: An Introduction and Resource Guide http://www.colostate.edu/programs/lifesciences/TransgenicCrops/ This site provides perspective and balance to the public debate and concerns over genetically modified plants. Set up by crop scientists from the University of Colorado, the site contains a wealth of information for students and the public about virusresistant papaya, Bt corn and many other genetically modified crops. Highlights include a lively animation that provides instructions on how to make a transgenic plant as well as a discussion of the risks and concerns posed by this technology. A host on links is provided to related pages, including those of groups opposed to genetic engineering. Bioengineering Action Network of North America http://www.tao.ca/~ban/ Just in case you thought the furor over genetically modified plants was beginning to cool, you may want to visit the web site of the Bioengineering Activist Network. This group advocates the destruction of transgenic plants and associated research materials in commercial, private, public, and academic settings. The web site provides regular updates on anti-biotech demonstrations and property-destruction actions. Detailed instructions are given on how to destroy genetically modified crops.