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The Soybean GBrowse Database

SoyV4R4 (Version 4 Data, Round 4 Programming)

The Soybean GBrowse Database combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. This customized database provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. Clicking on certain features also searches our database for listings of these relationships.

Note that the soybean genome is comparatively large, approximately 1,112 MB; a diploidized tetraploid, the product of two genome duplications that occurred 8-10 MYA and 40-50 MYA; extensively segmented and reshuffled; and, 64 percent euchromatic and 36 percent heterochromatic. The methodology for converting our data into a format GBrowse can use is explained futher below.

"You must know the ontology to use SoyV4R4." Ontology
Soybean Genome Browser
 
Summary
 

Methodology

The methodology is described in rounds of development. The most recent data is SoyV4R4 (Version 4 Data, Round 4 Programming)

SoyBase at Iowa State University   Left, soybean data is also at SoyBase at Iowa State University
GMOD Home Page   Left, the GBrowse Generic Genome Browser was used for our soybean database. the GBrowse web site is here. Also, see Stein
 
GBrowse is a part of the GMOD system. The GMOD web site is here.
 
A look at the GBrowse code.

 

Acknowledgment and Disclaimer

This material is based upon work supported by the National Science Foundation under Grant No. 9872635.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

 
 

              Deepak
http://soybeangenome.siu.edu
Last update: July 31,2005.