Description
The Agricultural Genome Information Server (AGIS) provides
genome databases of agriculturally important plant and animal
(Sept. 1995) species, and model organisms. The plant species include
alfalfa, Arabidopsis, common bean and soybean, Chlamydomonas,
cotton, small grains (wheat, barley, rye, etc.), maize, rice,
tomato, potato, pepper, sorghum, and forest trees. Also included
is Mendel, the database from the Commission on Plant Gene Nomenclature.
The WWW versions of the databases are provided in ACEDB format and are browsable via hypertext links. They are also searchable via WAIS, fuzzy searching (agrep), and querying through ACEDB (query by example, query builder, and ACEDB query language).
The databases are characterized by links to external databases,including EMBL, Enzyme Data Bank, Genbank, Genobase, GRIN (Germplasm Resources Information Network), Kyoto Ligand Database, Medline, PDB (Protein Database), PIR (Protein Information Resource), Prosite, Rebase, Selkov Enzyme and Metabolic Pathways, and SwissProt, and toolsare provided to enhance and augment external connections.
Documentation on the server includes a full suite of ACEDBdocumentation, electronic newsletters, journals, and otherpublications including: Plant Genome meeting abstracts, Weeds World, the Rice Genetics Newsletter, Report of the Tomato Genetic Cooperative , and the announcement for the new peer-reviewed electronic journal, The Journal of Quantitative Trait Loci.
As a novel extension of ACEDB for non-genome databases, several plant databases are provided, including PhytochemDB (plant phytochemicals), EthnobotDB (world wide plant uses), FoodplantDB (Native American food plants), MPNADB (Medicinal Plants of Native America), and PVP (Plant Variety Protection - soybean subset).
The AGIS is a service provided by the U.S. Department of Agriculture's National Agricultural Library in Beltsville, Maryland, USA. Funding is provided through the USDA, Agricultural Research Service, National Genetic Resources Program.
Access
The AGIS is located at WWW http://probe.nalusda.gov/
NOTE: If you do not have a WWW browser, but have telnet capability,
use the lynx, text-based browser. Telnet to probe.nalusda.gov
and use the login "lynx" (no quotes). No password is
necessary. You MUST use vt100 terminal emulation in order to use
lynx. Also, lynx has been modified so you can only browse the
AGIS along with a few related servers:Gopher: probe.nalusda.govAnonymous
ftp: probe.nalusda.gov
For More Information
Send comments to: feedback@probe.nalusda.gov
Send requests for help to: help@probe.nalusda.gov
Genome Informatics Group
USDA, National Agricultural Library10301 Baltimore Blvd.Beltsville,
MD 20705
The AtDB Project at Stanford
AAtDB (An Arabidopsis thaliana Database) and associated
WWW, Gopher and ftp resources have recently been transferred from
MGH/Harvard to Stanford.
With this move comes a change in title and its meaning. The AAtDB
name, which in the past has represented the name of the formal
database, will not be used. The Stanford effort will be known
as the Arabidopsis thaliana Database Project or AtDB (one A).
The name AtDB will be used for all aspects of the Stanford effort
including a formal database, WWW and Gopher search facilities
to Arabidopsis literature and electronic manuals, plus a variety
of future analysis-resources. The AtDB name is thus not just a
database, but a collection of information and analytical resources
maintained by the Stanford project.
A small proportion of the NSF-funded project is to maintain and
distribute the information previously collected by the AAtDB group
in Boston. This includes the following.
Description of AAtDB
The latest version of AAtDB is available for UNIX and
Macintosh operating systems. To get your own copy of the software,
connect via either ftp or WWW to genome-ftp.stanford.edu
. Other sites are listed below. The information is also available
through the Internet using the Gopher and WAIS software clients.
Special features of the latest release include:
Numbers of Objects in selected Classes for version 3-6:
Map 31
Allele 1334
Author 5981
Clone 23168
Contact 1447
DNA-Resource 2869
Gene-Class 244
Gene-Product 830
Germplasm-Resource 3520
Image 819
Journal 411
Locus 1988
Map-Population 26
Motif 349
Paper 4441
Probe 528
Sequence 41755
Sequence-EST 18277
Sequence-Homol 20780
Sequence-Genomic+ 2665
Source 61
2-point-data 4877
AAtDB features a wide variety of public information that is presented using graphical, text, and tabular formats. The user interface, which was designed to invite browsing, allows users to explore information by pointing and clicking with the workstation mouse or by using a versatile query facility. This UNIX release of AAtDB runs using the ACEDB 3.0 software. ACEDB allows all parts of the database to be cross-referenced with each other. The large number of interconnections provides a dense navigable network in which information can be located from many different starting points.
All information contained within AAtDB was obtained directly from the original authors or from publicly available collections and databases. Updates to AAtDB are made periodically, the current version of the database is 3-6. The next update should be early this year (1996).
The database features:
AAtDB uses the ACEDB software developed by Richard Durbin (MRC-LMB, Cambridge, U.K.) and Jean Thierry-Mieg (CNRS, Montpellier, France). Precompiled executables of ACEDB are available for Sun SPARC (SunOS and Solaris), DEC Alpha, and Silicon Graphics workstations under the X-windows environment. Source code is available for compilation with other computer architectures.
All the AAtDB information in text form is available from AtDB the Arabidopsis thaliana Database, at Stanford. The images obtained from the ABRC at Ohio State University and the Nottingham Arabidopsis Stock Centre (NASC) are available as via Gopher and anonymous ftp from the hosts genome-ftp.stanford.edu and genome-gopher.stanford.edu.
Connecting via the Web
The AtDB is also connected to the World Wide Web. The
URL is
http://genome-www.stanford.edu/
.
If you are unfamiliar with ACEDB software, there is a revised
version of the primer "An Introduction to ACEDB for AAtDB,
which is available through the Web server (URL=http://genome-www.stanford.edu/Arabidopsis/introaatdb/).
This manual is approximately 20 pages of text and graphics which
briefly describes the data and how to use the database.
How to obtain the Unix version of AAtDB:
UNIX files are available via anonymous FTP from three
sites. Note the new UK site at the European Bioinformatics Institute,
the URLs are:
ftp://ftp.ebi.ac.uk/pub/databases/ace/aatdb
ftp://ncbi.nlm.nih.gov/repository/aatdb/aatdb.3x
ftp://genome-ftp.stanford.edu/arabidopsis/aatdb/aatdb.3x
Detailed information about how to retrieve the Unix update information is included in the file AAtDB.Retrieval_Installation_ver_3-6 available via anonymous ftp on the AAtDB server (genome-ftp.stanford.edu, in the /arabidopsis/aatdb/aatdb.3x directory) . You will need to obtain the INSTALL script, the compressed binary for your machine and the update files. currently we have binaries for Sun Sparc running Sun OS or Solaris, DEC mips and alpha and SGI. You will need approximately 400 Mb of disk space to load and install, approximately 310 Mb final if you download all the image files.
How to obtain the Macintosh version:
Macintosh files are available from;
ftp://ncbi.nlm.nih.gov/repository/aatdb/MacAAtDB
ftp://genome-ftp.stanford.edu/arabidopsis/aatdb/MacAAtDB
To install the Macintosh version you need only retrieve the file MacAAtDB.sea.bin (using binary mode if you are retrieving with ftp). On the anonymous ftp server, the file is in /arabidopsis/aatdb/MacAAtDB. Double clicking on the file should launch the extraction process. Two version are available; one with EST sequences and homology data, and one without. The 'full' version requires 142,456 kb of disk space and the 'demo' version requires 52,587 kb of disk space. Neither version has the entire set of Stock Center images due to space limitations.
This is the first AtDB update from David Flanders and Mike Cherry,
Dept. of Genetics, School of Medicine, Stanford University, Stanford,
CA 94025.
Thanks to those that have submitted information, and especially
to the previous keepers of AAtDB: John W. Morris and Howard M.
Goodman, MGH/Harvard.
Please send all correspondence regarding AtDB to: atdb-curator
Description
CottonDB was recently constructed under a project sponsored
by the United States Department of Agriculture (USDA), Agricultural
Research Service (ARS) and was released to the National Agricultural
Library (NAL) Agricultural Genome WWW Information Site to serve
as a resource on the developing knowledge base of Cotton Genetics.
The collection of information to be entered into CottonDB may also be carried out over the World-Wide-Web using form pages at the designated CottonDB Data Collection Site. Forms are available for inputing information about COLLEAGUES, LITERATURE, RESEARCH, and other COMMENTS by accessing the URL: http://algodon.tamu.edu/
The RESEARCH form is set-up to speed entry of information about cotton genetics, plant-microbe interactions, metabolic pathways, sequence information and other observations.
Presently, CottonDB (version 95.1) is based on ACeDB version 3.0 (Richard Durbin and Jean Thierry-Mieg, MRC LMB Cambridge, England and CNRS, Montpellier, France, respectively) with modifications to AGsDB 1.0 (Leland Ellis, Chris Floyd, Janis Bender and Jeff Kirk, IBT TAMU, Houston, TX). Other plant genome databases were used as models in setting up some of the data entries.
At present, CottonDB ver. 95.1 (10 Janurary 1995) contains:
Colleagues: 1150 names and addresses of cotton- associated
people
Papers: 7208 Cotton-related Agricola and direct-entry
literature
Pathology: 284 Biotic and abiotic factors associated
with cotton
Trait Scores: 22380 Germplasm yield, fiber, and seed
data (detailed)
Collection: 613 Germplasm Resource Information Network
(GRIN) entries
Authors: 8265 Authors associated with Paper entries
Loci: 962 Observed and molecular markers
Sequence: 73 Cotton-associated sequences from GenBank
and others
Journal: 805 Journal headings
Trait Study: 1029 Traits associated with GRIN entries
Map: 98 Maps for observed and molecular markers
A revised version of CottonDB is planned using ACeDB version 4.0. This revised release will contain updated information about molecular markers, germplasm collections, species descriptions, nucleic acid sequences, and literature. It is hopeful that usage of the CottonDB Data Collection Site will speed access and availability of up-to-date research information. A short description of the CottonDB 95.1 database is available at: http://algodon.tamu.edu/homepage/lazo/docs/acedb95.html
Access
CottonDB is accessable over the World-Wide-Web at the
URL: http://probe.nalusda.gov:8300/index.html
For More Information
Contact, Gerard R. Lazo, Research Geneticist & Curator lazo@tamu.edu
Sridhar Madhavan, Graduate Research Assistant & Curator msridhar@tamu.edu
Russell J. Kohel, Director & Research Leader rjk0339@acs.tamu.edu
USDA ARS
Southern Crops Research Laboratory
2765 F&B Road, Building #11
College Station, TX 77845-9593
Phone: 409/260-9311
Fax: 409/260-9333
Description
The Dendrome project is based at the Institute of Forest
Genetics of the USDA Forest Service Pacific Southwest Research
Station, in Placerville and Albany California. The project aims
to provide a central electronic resource for the study of the
molecular biology of forest trees. Funding for the project comes
from the USDA Plant Genome Research Program and the USDA Forest
Service.
TreeGenes is a repository of genetic maps and associated information about species, germplasm, laboratories, researchers, probes, protocols, loci, DNA sequences, publications and more. It employs the ACEDB database software. The entire database is available for anonymous ftp, and a variety of access mechanisms are available through the World-Wide Web.
Over 2000 images of autoradiograms, rangemaps, and species are included. The project maintains the ACEDB Frequently Asked Questions documentation.
The Dendrome Forest Tree Research Updates is published twice per year and includes short articles concerning tree molecular biology. All issues can be accessed via WWW or Gopher. Researchers can be included on the mailing list by sendinge-mail or surface mail to the project.
A variety of detailed laboratory protocols related to tree molecular biology research are available. Expressed sequence data and gene family identities and information about commercially available 10-mers for PCR are included.
A Calendar of upcoming events is provided and a searchable bibliography is available on the Gopher server.
In coordination with F. Thomas Ledig, Dendrome has updated the IUFRO World Directory of Forest Geneticists and Tree Breeders. This directory can be searched via WWW. A paper edition is planned. About 2000 researchers have contributed biographical and research interest data to the collection.
The California Flora Database contains geographic and ecological distribution information for 6717 California vascular plant taxa, as well as additional habitat information for rare taxa and species of the Sierra Nevada. The entire database is available for anonymous ftp or can be searched via WWW.
Access
The project coordinates data with the Agricultural Genome
Information Server at the National Agricultural Library, Beltsville
Maryland. All services of the Dendrome project can be explored
via the World-Wide Web at URL: http://s27w007.pswfs.gov/
We also maintain Gopher servers at s27w007. pswfs.gov port 70 and at probe.nalusda.gov port 7508
For More Information
Email can be sent to dendrome@s27w007.pswfs.gov
Surface mail to Dendrome, Institute of Forest Genetics, PO
Box 245, Berkeley, CA, 94701, USA.
Description
GrainGenes is a central repository for information about
wheat, barley, rye, triticale, oats, sugarcane and related wild
grasses. GrainGenes includes genetic and cytogenetic maps;information
on mapping probes (including nucleotide sequences and digitized
images of mapping data); information on genes, alleles and gene
products; genotypes and pedigrees of cultivars, genetic stocks,
and other germplasms; information on phenotypes, quantitative
traits and QTLs; images depicting plant morphology and pathology;
addresses and research interests of colleagues; and relevant bibliographical
citations.
Access
GrainGenes is currently available in two formats (ACEDB
and Gopher) and a Web Server Home Page is under development.
ACEDB format:
Graphical user interface format; multi-windowed, mouse-controlled
environment with both graphic and text displays.Connections are
made between related pieces of information by clicking on data
objects with a mouse. The ACEDB format allows users to perform
sophisticated queries of the database and is available to users
with direct TCP/IP Internet connections and Xll graphics capability
(Unix workstations or most personal computers with inexpensive
software).
Gopher format:
Text interface format; menu-driven, displays all information
as text and contains tabular data and text documents not available
in the ACEDB format, some of which can be searched, downloaded
or browsed. This format allows for fast searching by any word
in the text and can be accessed with a modem connection to an
Internet host. There is enhanced capability to download and view
images.
The GrainGenes Gopher at greengenes.cit.cornell.edu contains the latest version of the GrainGenes ACEDB dataset in searchable form as well as a variety of information about wheat, barley, oats, and sugarcane in simple text or tabulated formats. Many of the files can be browsed, searched or downloaded to your own computer.
A sampling of the data offered as of June 1994 follows:
Search the following files by any word in the text:
Browse the following data files:
Download the following data to your own computer:
The GrainGenes ACEDB Database:
Version 1.4 of the GrainGenes ACEDB Database, a central repository
for information on wheat, barley, oats, sugarcane, and other small
grains, was released on October 28, 1994 and contains 22 maps
and 163 mapped linkage groups; more than 3,300 loci and 600 genes;
more than 2,400 probes with nucleotide sequences from the ends
of 100 probes; information about 22,000 wheat, rye and triticale
germplasms; information about 1400 plant, pathogen, and insect
species; 14,000 trait scores from the International Spring Wheat
Yield Nursery Trials; 450 pathology entries, many with digitized
images of disease symptoms; names, addresses and research interests
of more than 950 colleagues and more than 1,400 references.
For More Information
David E. Matthews (curator)
Dept. of Plant Breeding and Biometry
Cornell University
Ithaca, NY 14853
Phone: (607) 255-9951
E-mail: matthews@greengenes.cit.cornell.edu
Olin D. Anderson (coordinator)
USDA-ARS-WRRC
800 Buchanan Street
Albany, CA 94710
E-mail: oandersn@wheat.pw.usda.gov
Description
The Maize Genome Database or MaizeDB provides free, up-to-the-minute
information about the maize genome and is a component of the Plant
Genome Database network of the National Agricultural Library.
Over the past 1.5 years, use of the database has grown from 100-200
transactions/month to some 20,000. Information input and database
design are a cooperative on-line effort of several persons, both
on and off-site.
In June 1995, the database contained over 104,000 records describing 3059 mapped genes and gene candidates, 19821 genetic variations (including allozyme typing for 21 loci and 437 elite stocks), 2465 molecular probes, 240 genetic maps, 2966 raw map data entries, 33 QTL experiments (a new area this year), 1985 gentic/cytogentic stocks, 4662 elite stock pedigrees, 2430 addresses of research workers, and 6700 bibliographic references which increase by over 800 annually and are connected with the other database objects, including agronomic traits such as pest and disease responses.
Individual MaizeDB records are hard-linked over the World Wide Web to 18 external databases, permitting seamless retrieval of nucleotide and protein sequences, motifs, germplasm, related genes and/or sequences of other species and certain full journal articles.
Access
To connect, use any computer with a connection to the
Internet, including by modem.
Telnet to: teosinte.agron.missouri.edu
(For Web, gopher, or direct access to relational query forms.)
a. login: guest
b. password: corncob
If using your own Web or gopher software, connect to: http://www.agron.missouri.edu or gopher.agron.missouri.edu, respectively.
For More Information
For assistance or any comments, please contact the curator:
Dr. Mary Polacco, aryp@teosinte.agron.missouri.edu
Fax: 314/ 874-4063.
Description
RiceGenes is an internationally accessible computer database
containing a wide variety of information pertaining to rice genetics.
It is organized around the basic concept of a genetic map, with
markers on the map providing "hot links" to related
pieces of information such as marker sequences, vectors, homology
to known genes, and map locations in other species. The links
allow the researcher to move seamlessly among related items of
interest.
The database currently consists of information on over 3,000 DNA markers (including a contact person for acquiring probes or additional information); 5 genetic maps of rice (including the classical morphological linkage map and molecular maps developed at Cornell, in Tsukuba, Japan, and in Beijing, China); a genetic map of maize; relevant bibliographic citations; digitized images of autoradiograms; disease symptoms; and plant morphologies; and over 1,300 DNA sequences.
The database also includes RFLP profiles of rice germplasm, information about genetic stocks, and sequence information related to markers or known genes of rice. Detailed comparisons between the maize and rice maps have also been included. In collaboration with other groups we hope to develop interrelated genome databases for important pests and pathogens of rice, such as blast and bacterial blight.
Access
RiceGenes is accessible via the Internet in 4 forms.
The easiest form is at a Gopher server. The Gopher interface is
menu-driven and can be used with only a modem connection to an
Internet host. The first 9 volumes of the Rice Genetics Newsletter
are currently available as text documents on the Gopher server.
Preindexed for fast searching on any word in the text, the Gopher
versions of such documents are expected to be more useful to a
wider group of people than printed versions.
The second format is a graphical user interface based on the ACEDB software, available to users with direct TCP/IP network connections and X11 graphics capability (most UNIX workstations, or personal computers with inexpensive software). The ACEDB format provides live graphics, photographic images, and text displays, with hot links between data objects that can be activated by clicking with the mouse.
The third format is a World Wide Web server, maintained by the USDA/NAL. This is also a graphical inter-face and provides the capability of hot links between, in addition to within, databases.
The final format is an electronic mail query capability, for users who do not have full Internet access, but do have Internet mail service.
For non-Internet sites, the U.S. National Agricultural Library has made available a CD-ROM which contains all the USDA-funded genome databases (rice, maize, wheat and other small grains, arabidopsis, and many more).
Access points:
ACEDB version - UNIX version available via anonymous ftp from:
probe.nalusda.gov directory /pub/rice
WWW version - URL http://probe.nalusda.gov:8000
Gopher version - gopher nightshade.cit.cornell.edu port 70
WAISmail - send mail to waismai@probe.nalusda.gov with just the
word help in the body.
For More Information
Edie Paul (curator)
Dept. of Plant Pathology & Biochemistry
Cornell University
Ithaca, NY 14853
Phone: 607/255-9951
E-mail: epaul@nightshade.cit.cornell.edu
Susan McCouch (PI)
Dept. of Plant Pathology & Biochemistry
Cornell University
Ithaca, NY 14853
Phone: 607/255-0420
E-mail: srm4@cornell.edu
Description
SolGenes is one of three plant genome databases, based
on the ACeDB software and funded by the USDA's Plant Genome Project,
that are maintained at Cornell University. The scope of SolGenes
is the solanaceous crop species - presently including tomato (Lycopersicon
spp.) potato (Solanum spp.), and pepper (Capsicum spp.) - and
their wild relatives.
Genomic research data from other Solanum species (such as S. melongena, eggplant) and other genera in the family (Datura, Petunia, and Nicotiana for example) are also invited. The core of SolGenes consists of genetic maps, displayed in ways that allow ready cross-referencing. Presently available are various tomato, potato, and pepper RFLP maps constructed at Cornell and elsewhere; others are being added.
Users may search a catalog of more than 3000 tomato genetic stocks (mutants, chromosome testers, sources of named resistance genes, etc.), maintained at the Tomato Genetic Resources Center (TGRC) in Davis, CA by R. Chetelat. A recently developed set of 50 L. pennellii single-segment introgressions into a L. esculentum background, characterized with some 350 RFLP and isozyme markers and available from the TGRC, is shown graphically on the genome maps. There is ample scope for developing SolGenes as a tool for research into plant-microbe interactions; we haven't pursued this prospect yet but invite discussion.
Entries are cross-referenced against a background of literature citations (130), a colleague directory (541), and catalogs of probes (1000), loci (2000), and restriction enzymes (340).
Access
The entire database may be obtained via anonymous ftp
from probe.nalusda.gov:pub/solgenes, if you wish to set it up
on a local (typically Unix-based) computer. There is also a Macintosh
version of ACeDB called MacAce, but the SolGenes data are not
yet available on this platform. You can access SolGenes via a
text interface through either of these Gopher servers: nightshade.cit.cornell.edu
port 71 or probe.nalusda. gov port 7006
The text-based ways of accessing the database don't offer the graphical displays available with a version running locally, although data and images are retrievable. An X-window emulator program running on your local PC or Macintosh (MacX for example) will provide, via remote logon, the full range of graphical displays built into ACeDB databases. Another route is via Netscape or the World Wide Web URL: http://probe. nalusda.gov:8300
For More Information
Messages may be sent to other SolGenes users at solfolk@nightshade.cit.cornell.edu
To be placed on thismailing list or to obtain further information
about SolGenes, write the curator (Clare Nelson) at jcn5@cornell.edu
or cnelson@nightshade.cit.cornell.edu
Several scientists in the U. S. and Europe have agreed to serve on an informal steering committee for SolGenes and can assist as liaisons with Solanaceae workers. They are: for potato, Herman van Eck, Wageningen, Netherlands Herman.vanEck@ users.pv.wau.nl for pepper, Molly Kyle, Cornell mmk9@cornell.edu and Paul Bosland, New Mexico State pbosland@ nmsu.edu for tomato, Pim Lindhout, Wageningen Pim.Lindhout@users.pv.wau.nl , Roger Chetelat, UC Davis chetelat@vegmail.ucdavis.edu and Martin Ganal, Inst. f=FCr Pflanzengenetik, Gatersleben, Germany, Fax: 49-39482-280.
Description
SorghumDB is a joint project of USDA National Agricultural
Library and Texas A&M University. This is a part of the Genome
Database Project of NAL. It is curated by Najeeb Siddiqui under
the supervision of Dr. Keith Schertz at Texas A&M University
and supported by a whole group of scientists with interests in
sorghum breeding, pathology, physiology, genetics, etc. Sorghum
Genome Database Project was started June 1994. Since then, an
experimental version of SorghumDB was released in January, 1995
and a complete version 1.0 was released in May, 1995. Version
1.1 is expected to be released by the end of August, 1995.
SorghumDB contains a wide variety of information on topics such as genetic maps, germplasm, gene loci, alleles, pathology/pathogens, taxonomy, multi-maps (sorghum vs. maize), etc. It is also a good source of reference information for papers published in any research area of sorghum, and for the most updated information on colleagues working in sorghum research.
We have tried our best to include as much text information as possible on topics like germplasm, traits, pathology, and taxonomy with complete references to the source of the data. Included are all 108 RFLP maps of sorghum linkage groups and 12 multi-maps between sorghum and maize; a description of maturity alleles; a detailed description of all sorghum cultivar, germplasm, parental lines, genetic stocks, and converted lines; information on gene loci and RFLP probes; a description of sorghum diseases and sorghum pathogens; hierarchical description of sorghum taxonomy; reference information on approximately 11,000 authors and more than 10,000 published papers in various areas of sorghum reasearch, representing about 1,400 different journals and books.
We have more information on the existing classes of the database that will be incorporated and we also have some new classes in our plans which will be included in the future versions of the database.
Access
SorghumDB can be accessed from the ACEDB Moulon Server
at NAL by connecting to http://probe.nalusda.gov:8300/
ACEDB 3.0 format of SorghumDB is available by anonymous ftp from the National Agricultural Library at probe.nalusda.gov in the pub/sorghumdb directory. It requires a UNIX machine.
To download the database, type at the prompt:
a. ftp probe.nalusda.gov
b. anonymous
c. your e-mail address
d. binary
e. cd pub/sorghumdb
f. get sorghum-june-95.tar.Z
(Login ID is anonymous and Password is your e-mail address)
After the transfer is complete, type bye to quit the session.
For More Information
Contact:Najeeb Siddiqui
Sorghum Genome Database Curator
Crop Biotechnology Center
Texas A&M University
College Station, TX 77843-2123
Phone: (409) 862-1523
Fax: (409) 862-4790
E-mail: najeeb@genome.tamu.edu
or nus6389@tam2000.tamu.edu
Description
Soybase is an ACe-type genetic database with hypertext
links between topics. It currently contains approximately 100
megabytes of data including, but not limited to:
Genetic Maps
The classical gene map contains 29 linkage groups and
the underlying 2 point linkage data is in the database. The four
molecular maps represent independent mapping populations with
significant overlap between the markers used. Images ofautoradiograms
are available which indicate the exact DNA fragment that was used
to place an RFLP marker on a map. Related information about genes,
alleles, and molecular probes is available via hypertext links
from the map diagrams.
QTL Studies
For each QTL study there are data on the trait evaluated,
the population used and the associations between the phenotypic
traits and the molecular markers. A hypertext link is available
between these linked loci and the genetic map diagrams.
Metabolic Pathways
There are diagrams covering forty-one pathways for nitrogen
and fatty acid synthesis and degradation. For each pathway, information
is available for the enzymes, reactants, products, and cofactors
involved along with the data on the kinetics,inhibition, activation,
and regulation of the enzymatic steps. More than 200 individual
enzymes are detailed.
Pathology and Diseases
Fifteen soybean diseases are covered in Soybase, including
data on the causative organism, differentials and phenotypic scores,
and the genetics of resistance.
Nodulins
Soybase currently includes information on 37 nodulins.
Examples of the data available are the nature of the gene product
encoded by the nodulin gene and its function, thehost and inducing
species, and information on the genetics and genome organization
of the gene.
References
All references in AGRICOLA that are related to soybean
genetics are incorporated into the database. In addition, other
peripherally related references such as those for heterologous
probes or metabolic data from other species are included.
Access
You can access Soybase in several ways. If you use a
Macintosh or PC, options 1 and 3 require that you run an X-windows
program on your local computer, as well as a WWW browser or Telnet
client.
For More Information
Contact:David Grant
USDA-ARS
G 304 Agronomy Hall
Iowa State University
Ames, IA 50011-1010
Phone: 515/294-1205
E-mail: dgrant@mendel.agron.iastate.edu
Randy Shoemaker
USDA-ARS
G 401 Agronomy Hall
Iowa State University
Ames, IA 50011-1010
Phone: 515/294-6233
E-mail: rcsshoe@iastate.edu
Marcia Imsande
G 302 Agronomy Hall
Iowa State University
Ames, IA 50011-1010
Phone: 515/294-1297
E-mail: mimsande@mendel.agron.iastate.edu
Dave Schrader
G 316 Agronomy Hall
Iowa State Univesity
Ames, IA 50011-1010
Phone: 515/294-0421
E-mail: schrader@mendel.agron.iastate.edu