The Sequence Window I
The sequence window illustrated in this figure shows an overview of the chalcone synthase DNA sequence. The same sequence window could have been opened directly from the Sequence class, or from the tt4 text window (discussed earlier when we looked at the genetic map), or from other windows.
What is seen for a given sequence window depends on what is known about the sequence from the DNA sequence database. For example, because the intron-exon structure of the chs gene was described by the authors in their GenBank submission, it is represented (in blue outlines) to the right of the coordinate axis. Exons are the boxes, while introns are represented by the lines between the boxes.
The sequence window resembles the genetic map window, and some of the controls and buttons are similar. To the left is a coordinate axis with a slider bar (used to recenter the display), and the buttons Whole, Zoom In, and Zoom Out adjust scale. The yellow bar next to the coordinate axis is a linear representation of the sequence (ACeDB will use it to show, among other things, the recognition sites for a restriction enzyme). The sequence window also has its own menu, which has been popped up for you to see.
The Columns button controls the visibility of several kinds of information in the sequence window. (We will describe selecting features with the Columns button on the next page.) The first feature is a block of text which is in the right half of the display. Its size will vary with the sequence. These terms are links to other information in AAtDB and they behave as if they were in a text window. Double-clicking on a term will open new text windows, the genetic map, or the physical map. For example, clicking on "Clone: chs" will open a window showing the physical map associated with the sequence; clicking on the Paper class item (feinb-1988-aaaph) will open a text window showing the complete citation for that bibliographic reference.
A second kind of information controlled by the menu under the Columns button is the crowded group of vertically-oriented rectangles which, in this example, lie to the right of the intron-exon structure. This is the "Peptide Similarity" feature on the Columns button menu. Each rectangle represents a BLASTX-identified similarity between the chalcone synthase DNA sequence - translated in all six frames - and all known protein sequences from the Swiss-Prot, PIR, and GenPept protein databases. The blocks show which regions of the chalcone synthase sequence at the protein level are similar (based on certain significance rules) to proteins in the databases mentioned above. Details about each match are available by clicking twice on the similarities rectangle with the leftmost mouse button to bring up a text window.
Before we leave this example, notice that the sequence window's title bar contains the sequence name, which is the same as the Genbank Locus name, in this case ATHCHS. Clicking on the sequence name (ATHCHS) at the top of the text area will bring up a text window which includes the GenBank accession number as well as other data.
The Columns button also controls the display of the actual sequence. Click once on the Columns button with the leftmost mouse button to produce the figure on the next page.