mcclean at PROBLEM_WITH_INEWS_DOMAIN_FILE
Fri Mar 3 17:33:31 EST 1995
BeanGenes --- A Phaseolus/Vigna sp. Database
Phillip E. McClean
Department of Plant Sciences
North Dakota State University
Fargo, ND 58105
mcclean at beangenes.cws.ndsu.nodak.edu
Plant Genome Databases
Plant genome databases have been designed for a number of important crop
species. The goal of these databases is to provide "one-stop shopping" for
information that is relevant to a species or group of species. Examples of
these databases include GrainGenes (for cereal groups), SolGenes (for
Solanaceous species), and SoyBase (for Glycine species). Information that is
contained in these databases include molecular mapping data, germplasm
information, trait studies, identified quantitative trait loci, pathogen
descriptions, relevant publication citations, images pertaining to all aspects
of the crop, and colleague addresses. These efforts are each funded by the
USDA Plant Genome project.
BeanGenes is a plant genome data base which currently contains
information relevant to Phaseolus and Vigna species. The BeanGenes project
was funded by the USDA/ARS Plant Genome project through the SoyBase project
administered by Dr. Randy Shoemaker (USDA/ARS, Ames, Iowa). The hardware
component of BeanGenes is a computer containing a Pentium P90 processor, 64
mByte RAM, 2 GByte hard drive, and 8 GByte tape backup drive. The machine is
running under the Linux operating system. Linux is a Unix-based operating
system designed to run on machines using the Intel X86 series of processors.
Internet domain name of the machine is beangenes.cws.ndsu.nodak.edu. The IP
address of the machine is 220.127.116.11.
Currently, all of the BeanGenes information is stored in the ACeDB
software application. This is the most frequently used plant genome database
application. Richard Durbin (MRC, England) and Jean Thierry-Mieg (CNRS,
France) initially developed ACeDB (an acronym for A C. elegans database) to
archive information about Caenorhabditis elegans (Durbin and Thierry-Mieg,
1995). The database runs under the X-Windows environment on machines
utilizing some flavor of a UNIX operating system. To access the database as
an X-window application, the user must login on the server. Alternatively, a
user can obtain a copy of the database and install it on a local X-Windows
server. Remote users will need to access the database from a computer running
a form of X-Windows. The database can be accessed from any personal computer
or MacIntosh computer which has X-Windows emulation software.
BeanGenes contains several classes of information. All of the published
molecular maps of P. vulgaris are represented in the database. These include
the restriction fragment length polymorphism (RFLP) map developed by Dr.
Eduardo Vallejos at the University of Florida (Vallejos et al., 1992) and the
RFLP map developed by Dr. Paul Gepts at the University of California, Davis
(Gepts et al., 1993). The combined RFLP and randomly amplified polymorphic
DNA (RAPD) developed by Dr. Michel Dron at University of Paris, Sud can also
be accessed. Dr. Nevin Young of the University of Minnesota has provided RFLP
maps of mung bean (Vigna radiata) and cowpea (V. unguiculata).
Associated with each molecular map are loci and probe information. The
loci information describes the probes or RAPDs used to define the locus, and
the probe data provides specific information about a given probe.
BeanGenes also contains all of the gene information that was complied by
Dr. Mark Bassett, University of Florida. This is identical to the recent
published list (Bassett, 1993) All published references to the genes are also
The BeanGenes database can be accessed in three manners. For those
users with X-Windows capability, a login on the BeanGenes server can be
established. If you would like to have an account on the BeanGenes machine
contact Phil McClean at mcclean at beangenes.cws.ndsu.nodak.edu and an account
will be established.
Two methods of accessing the database are available that do not require
X-Windows capability. The ACeDB form of BeanGenes can be searched on the
Agricultural Genome World Wide Web Server at URL
http://probe.nalusda.gov:8300/. This WWW site can be accessed by such client
software as Mosaic and Netscape. Once the site is reached, find the BeanGenes
entry and the database can be navigated using standard point-and-click
The database is also accessible using the Gopher application.
The gopher address is probe.nalusda.gov. When the database is accessed via
Gopher, the user will able to search for information using the WAIS (Wide Area
Information Search) application. Use the following menu steps to find the searchable
version of BeanGenes.
2. Plant Genome Informaton
2. Access to Genome Databases
19. Search BeanGenes (Phaseolus sp.)
Bassett, M.J. 1993. List of genes - Phaseolus vulgaris L. Ann. Report of
Bean Imp. Coop. 36:vi-xxiii.
Durbin, R. and J. Thierry Mieg. 1995. A. C. elegans database. Documentation,
code and data available from anonymous FTP servers at lirmm.lirmm.fr,
cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov.
Gepts, P., R. Nodari, S.M. Tsai, E.M.K. Kinage, V. Llaca, R. Gilbertson, and
P. Guzmán. 1993. Linkage mapping in common bean. Ann. Report of Bean
Imp. Coop. 36:xxiv-xxxviii.
Vallejos, C.E., N.S. Sakiyama, C.D. Chase. 1992. A molecular-marker-based
linkage Map of Phaseolus vulgaris L. Genetics 131:733-740.
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