Lesson 9 - Sequences

Tools and Techniques

In this lesson we'll continue moving to a finer resoluation of information - this time looking at DNA sequence data. This will again use the Arabidopsis database, which may have a slightly different looking web interface. We have now covered all the different query methods, so the examples may use any of the methods.

DNA sequence data

The ultimate physical map is the entire DNA sequence of a chromosome. Once the sequence is known, efforts can shift from finding genes to determining gene function. (It's one thing to identify a stretch of DNA as being a gene - it's another to determine what exactly that gene does.) While off to a relatively slow start compared to the Human Genome Project, the amount of plant sequence data being generated is rapidly increasing, and plant scientists are facing a deluge of data.

Even if the entire DNA sequence for a chromosome or even a single clone is not known, partial sequence data may be available. Often this is "end" sequence data, in which the ends of a fragment of DNA are sequenced. This partial sequence data may be used to design primers, or to determine overlap of clones. While the Arabidopsis database contains the greatest volume of sequence data, many of the other databases contain a significant amount as well. Sequence data may be linked to loci, probes, germplasm, maps - any number of objects; it may also have links into various external sequence-related databases, like GenBank, EMLB, DDBJ, and so on.

Just as with genetic maps, there is a special graphic display in ACEDB for sequence data, and many different "columns" of information may be contained in the display. The display may contain information about regions of homology (either sequence or protein) to other species, features (such as mutations, repeats, polyA signals) of the sequence, coding/non-coding regions, and so on. You may want to display the actual DNA sequence (or its reverse complement, the non-sequenced strand). The native ACEDB interface has even more functions that can be performed on sequence data, which are not available via the WWW interface.

Example 9.1 - We will look at DNA sequence data from several databases. The interface for Arabidopsis may be a little different, so be sure to read the instructions carefully. Check out as many as you like!

AGR
If you have an AGR Database comment or question contact David Flanders, Curator.