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 188.8.131.52.
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. 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.
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 firstname.lastname@example.org
and an account will be established.
Two other 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 techniques. 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.