Lesson 5 - Intervals on the Map - Cytological and Introgressed regions

Tools and Techniques

In this section we will start looking at interval data that may appear on or associated with a genetic map. Many different sorts of information could be represented as a particular region of a map, and we will start by looking at cytological regions and introgressed regions. We'll cover a new query method as well - a WAIS (Wide Area Information Servers) search.
 
 

WAIS searching

So far all our searches have been restricted to just a single class. In other words, you selected a particular class to search, for example Gene, and the result contained only Gene records. If your search criteria existed in other classes, they were not returned. This meant that you needed to be somewhat familiar with the contents of the database you were searching (one generally gets familiar with a database by using browse mode on it). The WAIS search method scans all the classes in one or more databases for your search terms, so it may return a mixture of different types of information, for example, you might get back Gene records, Locus records and Gene_Product records. WAIS searches are case-insensitive.

The WAIS search operates from an index that contains an entry for nearly every word in all the databases located on the AGIS server. You can run the search against a single database or multiple databases. If your query is successful you will obtain a list of objects that you can click on in the usual way to obtain additional information. If you have searched more than one database at the same time, the list may contain objects from different databases. The objects will be ordered by a relevance score, which reflects the number of times your search term(s) appears in each object. Only the top 40 hits from any database will be returned for a given search - keep that in mind if you are performing searches which return a large number of hits. Also, keep in mind that the structure of the data retrieved by WAIS varies between databases (there is no standard schema shared by the genome community), therefore query results will not be uniform across databases.

WAIS searching is appropriate when you don't really know which database class might hold the desired information, or what format it might take. It is useful for broad searching - when you want any possibly relevant record returned. The downside is that only the top 40 records are returned, so if you're searching on a common word or phrase, you may not be seeing all the possible records.

To perform a WAIS search you will need to enter your search term(s). By default WAIS looks for complete, exact matches. For example, if you enter photo, only objects that contain the word photo will be returned. An object containing the word photograph will not be detected. Partial word matching is provided by adding an asterisk "*" to the end of a word (e.g., photo*). Thus if your first search attempt returns nothing try the same word with an "*" at the end. Note: you can only use "*" to extend a word (i.e. it can only be placed at the end of the search term). *hoto and ph*to will not match photo.

If you enter a series of words (word1 word2 word3...) separated by a space or with commas, you will be returned a list of objects that contain matches to at least one of the query words. In this case WAIS is treating the list as if the Boolean operator OR were present between each search term (word1 OR word2 OR word3). (You can also specifically enter the operator OR if you wish.) A search may also use the operators AND and NOT. The AND operator means that both search terms must be present (word1 AND word2 returns only records containing both word1 and also word2). The NOT is used to exclude certain records (word1 NOT word2 returns records which do contain word1 but which do not contain word2). For complex queries, you can use parentheses to indicate which operators to evaluate first, for example "(sugar fructose) NOT sucrose" will return records that contain either sugar or fructose but which do not contain sucrose.

Literal phrase matching is performed when the search phrase is surrounded by either single or double quotes. For example, the search for "light harvesting" (including the quotes) will only return objects that contain that exact phrase. As noted earlier, a search without the quotes identifies entries that contain either the word light or the word harvesting.

Example 5.1 - The following example continues the explanation of WAIS searching and lets you try it out for yourself.

CottonDB
If you have a CottonDB Database comment or question contact Savita Kini, Curator.
 
 

Cytological regions

Cytology is the study of chromosomes and their structure. There are a number of different topographical "landmarks" which can be identified on a chromosome. The centromere region often appears as a constricted area, and is the dividing point between the two "arms" of the chromosome. During cell division, spindle fibers attach to the centromere and help move the chromosomes to the appropriate place in the cell. Nucleolar organizers (NORs) appear as secondary constrictions of the chromosomes. These nucleolar organizer regions contain the genes for ribosomal RNA, and their number and position in the genome is very specific to a species. Knobs are thickened regions of the chromosome, and chromomeres appear as beadlike thickenings during certain stages of cell division.

When chromosomes are stained with certain chemicals, different regions have different staining characteristics. Densely stained regions are called heterochromatin and poorly stained regions are euchromatin. The difference in staining is thought to reflect the degree of compaction of the DNA in that region. Certain organisms, such as Drosophila, have polytene chromosomes, which are bundles of replicated chromosomes that are all still attached to each other, making the chromosome longer and thicker. Patterns of bands, puffs and rings can be identified on these chromosomes.

Example 5.2 - The database below has examples that illustrate where to find and how to interpret information about cytogenetic maps.

GrainGenes
If you have a GrainGenes Database comment or question contact Gerry Lazo, Curator.
 
 

Introgressed regions

Introgressions are regions of the genome that can be traced to some particular ancestor. They may result from something like a random crossing to a wild relative, or a very carefully planned hybridization followed by a series of backcrosses to some desirable recurrent parent. Introgressed regions often contain one or more desirable genes.

Introgression lines are a series of plants derived from some hybridization, typically between a wild or unadapted source and a cultivated plant, in which each offspring plant contains one or more genomic regions from the unadapted parent. These lines can be useful breeding and mapping tools, making it possible to identify and locate desirable genes from the unadapted parent which might otherwise go undetected.

Example 5.3 - The database below has examples that illustrate where to find and how to interpret information about introgressed regions.

SolGenes
If you have a SolGenes Database comment or question contact Sam Beer, Curator.

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