Bioinformatics and its relevance to weed science

An overview of bioinformatics is presented with an emphasis on describing a set of tools, databases, and ontologies useful to the weed science community. These tools can be used to identify genes whose product may be the target site of a herbicide or in the degradation pathway of a xenobiotic. They may identify receptors responsible for pathogen recognition or enzymes in the metabolic pathway for allelopathic compounds. Whatever the gene of interest, bioinformatics allows researchers to assemble complete or partial genes from expressed sequence tags (ESTs), complete cDNAs, or complete genomes and then translate them into their corresponding amino acid sequences. Similarity searches can be used to find other proteins with homology to the gene of interest, which can provide clues to its function from the annotation of these database hits. The use of protein domain databases can also provide insight into the functional capabilities of the protein in question and delineate those portions essential for activity. Enzyme Commission (EZ) numbers or gene ontology (GO) descriptors allow placement of the protein within the larger network context of a biological system. These capabilities allow the scientist to probe deeper into the function of their protein of interest to gain a novel understanding of the biology.