Lesson 4 - Points
on the Map continued Lesson 4 - Points
on the Map continued
Tools and TechniquesIn this second part of lesson 4 you will learn how to use the Query Builder to get information from the databases. We will continue looking at objects that are assigned a single point position on a map, but now we'll focus on known genes. Known genes may be mapped or unmapped, and this lesson will include examples of both.
Some of the databases split genes out into a separate class, and some make genes a special type of locus. You should keep this in mind as you switch between databases, or if you can't find the information where you expect it.
Query BuilderThe Query Builder (QB for short) gives you a little more control over your query than does query by example (QBE another search tool discussed in the first half of this lesson). Like the query by example, QB is appropriate when you can be fairly specific in expressing what you want to find. You can access QB whether you entered a database in Browse mode or Query mode. QB searches are case-insensitive and are limited to a single class of information; in other words, you will be returned only one type of record, never a mixture. A main distinction between the QB and QBE is that with QBE all your restrictions are AND'd together, but with QB you can select whether to AND or OR the restrictions. You can also use a variety of different comparison operators, such as >, <, contains, and so on.
Example 4.9 - The following example continues the explanation of Query Builder and lets you try it out for yourself.
GrainGenes
If you have a GrainGenes Database comment or question contact Gerry Lazo, Curator.
Mapped genesIn general, the distinction made in most of the databases between a locus and a gene is that a gene has some known or suspected function attached to it. So as we investigate information about genes, we might expect to find descriptions of gene function, gene product and even metabolic pathways. In these first examples we'll look at cases where the gene has been mapped and has a known position on the genetic map, including rubisco in BeanGenes and a stem rust resistance gene in GrainGenes.
Example 4.10- The databases below have examples that illustrate where to find and how to interpret information about mapped genes. Investigate as many as you like!
GrainGenes
If you have a GrainGenes Database comment or question contact Gerry Lazo, Curator.
BeanGenes
If you have a BeanGenes Database comment or question contact Phil
McClean, Curator.
Unmapped genesSo far everything we have looked at, molecular markers and genes, have been tied to the genetic map. In many crops, however, historical information on genes affecting morphology may far exceed available map or segregation data. The databases vary in the degree to which they are "map-centric"; some may not contain any information on genes that are not mapped, others may contain quite a bit. The SorghumDB example looks at anther-related genes, the SoyBase example looks at storage protein genes.
Example 4.11- The databases below have examples that illustrate where to find and how to interpret information about unmapped genes. Investigate as many as you like!
SorghumDB
If you have a SorghumDB Database comment or question contact Najeeb Siddiqi,
Curator.
SoyBase
If you have a SoyBase Database comment or question contact David Grant, Curator.
Metabolic pathwaysSo far we have encountered a special graphic display for the genetic map only. Another display that is supported in the ACEDB software is for metabolic pathways, showing the reactants, products and enzymes involved. This might be something as involved as the Lipoxygenase pathway, or as straightforward as arginine degradation. The last example you looked at for SoyBase (4-11) brought you to the Enzyme class, which detailed a particular reaction that might be part of a larger pathway. The next example will take a closer look at reactions and pathways involved in nodulation, including the graphical display. This provides you with a larger picture of how different genes act together in complex metabolic processes. Different alleles at any of the many genes involved in a pathway may produce subtle or drastic effects on the phenotype of the organism.
Example 4.12- The database below has examples that illustrate where to find and how to interpret information about metabolic pathways.
SoyBase
If you have a SoyBase Database comment or question contact David Grant, Curator.
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