Tutorial: Editing Sequences

This tutorial focuses on the sequence editor. Together with Tutorial 1: Tour of a Gene Inspector Notebook and Tutorial 3: Using Analysis Setups, this tutorial provides an overview of the three main parts of the Gene Inspector.

  1. In this tutorial, you will learn how to open and manipulate sequences stored within Gene Inspector sequence files. Choose File Open and select and open the nucleic acid sequence called pBR322 (it is in the DNA folder in the GI Seqs folder). You will see the window shown in Figure 4. The name column contains the name of the sequence being displayed in the line to the right of the name itself. For single sequence files, like the pBR322 sequence shown in Figure 4, the sequence name is only shown on the first line of the sequence (a). The position column contains the position of the first nucleotide (or amino acid) in each line. The overview pane at the top of the window shows a graphical representation of the sequence. Within the overview pane, the dotted rectangle, called the segment indicator, indicates the segment of the sequence currently visible in the sequence editor window. The Sequence Display menu can be used to show or hide these different parts of the sequence window. Feel free to try different items in this menu at this time.
    Figure 4: Sequence Editor with a Single Sequence

  2. Scroll down the sequence by using the scroll bar on the right of the window. Notice how the segment indicator in the overview pane moves along as you scroll and indicates exactly where you are in the sequence.
  3. You can also navigate to different positions within the sequence by clicking with the mouse in the overview pane. The sequence editor will automatically scroll to the location in the sequence that was clicked in the overview and will also select the clicked sequence. You can even drag the segment indicator to navigate within the sequence part of the window. Try clicking in the overview pane of the window to navigate. Try dragging the mouse in the overview pane.
  4. Select 20-30 nucleotides by clicking and dragging the mouse over the nucleotides, just as you would in a standard text processor. Choose Format Color Red and notice the change. Now choose Format Style Bold. Notice that the sequences stay aligned even after making them bold – if at all possible, the Gene Inspector will keep your sequences aligned automatically.
  5. Select the entire sequence by choosing “pBR322” in the name column (on the left) and change the font to Times using Format Font Times (b). Notice how all the characters still line up appropriately even though you are using a proportional font (Times) instead of a monospaced font (Courier). You can deselect the sequence by clicking anywhere in the sequence itself, just like in a word processor.
  6. Select Sequence Show Sequence Monitor, which will bring up a palette like the one shown in Figure 5. The Sequence Monitorc shows relevant information about the sequence you are working with in the sequence window, it allows you to set some speech properties, and it provides two ways for confirming a sequence. The first way is simply to have the program speak the sequence to you (it will start reading at the beginning of the current selection in the sequence editor). The second way is to confirm by re-entry. With this method, as you type in the sequence a second time, the program will compare it with the characters you entered the first time. Any differences will be brought to your attention with a beep. The Map Keys… button allows you to redefine the keyboard for entering sequences more conveniently. The default values for the keyboard map are shown in Figure 5. The top of the figure shows the options for Windows XP, while the bottom figure shows options for Macintosh OS X.
    Figure 5: Sequence Monitor

  7. Select 5-10 lines of the pBR322 DNA sequence and then choose Sequence Manipulate Sequence Translate. Specify a translation table (the E. coli table might be appropriate for pBR322) and click OK . A new sequence window will be created containing a translation of the segment of DNA selected in the pBR322 window. Note that this is not the same as looking for an open reading frame but simply represents a translation of the selected nucleic acid sequence. Note that the DNA is translated in groups of three starting with the first nucleotide in the selected segment; any stop codon is indicated as “·”. Click on the name of the new peptide sequence in the new window and choose Sequence Sequence Info…. This shows information about the generated sequence and provides a text field for storing comments. Because the program generated the sequence for you, it also placed some appropriate comments in the sequence info box for you. Close the dialog box.
  8. Close the Sequence Monitor and then close the pBR322 sequence file and the generated “untitled” peptide window. Choose File Open… and open the peptide file called rhodopsins – it is in the Peptide Sequences folder inside the GI Seqs folder. This file contains multiple sequences and is shown in Figure 6 (d) . Note the overview pane of the sequence window. It now displays multiple sequences and indicates their relative lengths. The segment indicator box indicates which segment of each peptide is being displayed in the window. In this particular case, the first three sequences have four lines displayed and the last two sequences (Octopus and Xenopus rhodopsins) have only three lines displayed in the sequence pane. Scroll the window through the sequence file using the scrollbar on the right side of the window and note how the segment indicator indicates the visible sequences.
    Figure 6: Sequence Editor with Multiple Sequence File

  9. Click in the overview. Note how the position of the segment indicator changes and how the sequence that is the target of the click in the overview pane is now selected in the sequence editor part of the window. This navigational tool becomes more useful as you put more and longer sequences into the a single sequence file.
  10. You can try other formatting options in this window using available items in the Format menu (for example, you can change the color or style). To select an entire sequence, click on the name of the sequence in the name column. Note that in the multiple sequence file, each sequence line has a name next to it so that you are never confused about what you are viewing.

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.

a. Figure 6 shows a sequence editor document with multiple sequences – this will be discussed later.

b. Depending on your current configuration, you may see an “extra cautions” dialog. This is described elsewhere in the manual.

c. Being a “palette”, the Sequence Monitor always remains in front of other windows. It will reflect information about the active sequence window (the one containing the selection or insertion point). If a different sequence window is brought to the front, the information in the Sequence Monitor will change.

d. Your display might look slightly different from this figure.

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