Abstract
In bacterial artificial chromosome (BAC) based physical maps
of polyploid and paleo-polyploid genomes duplicated features
form a complex web of associations. BAC clones can have
multiple relationships with loci, contigs, Minimum Tiling
Paths (MTP’s), sequences, related genes, Expressed Sequence
Tags (EST’s), Quantitative Trait Loci (QTL’s), BAC end
sequences, and other features. Each feature, can have
multiple relationships with each additional features. The
aim of this study was to develop an ontology and methods to
describe, store, manipulate, retrieve, and display
relationships found in polyploid genomes. An ontology to
describe genomic relationships was developed. A SQL
multi-table database was created to store and query the
information. Extropy, object-oriented Perl software, was
programmed with heuristic algorithms to load the database,
facilitate the manipulation of the data, and create genomic
flat file (GFF) output. The GFF output represented tracks
suitable for displaying polyploid genomic regions in the
Genome Browser (GBrowse)and other tools. This visual output
greatly enables education, discovery, the generation of
hypotheses, and the motivation of new methods for data
analysis concerning the soybean genome. All data, source
code, and the GBrowse display are available at http://soybeangenome.siu.edu.
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Deepak
http://soybeangenome.siu.edu
Last update: July 31,2005. |
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