1. My system recently crashed and now when I try to launch Gene Inspector I get a “not able to locate a valid license file” error. What can I do?
Try performing a "Clean Installation" using the GI CD you were shipped.
First, we'll need to find and remove some "Preferences" files GI stores on your local hard drive:
Search the primary hard drive for a folder titled "Textco Preferences".
Macintosh path:
Macintosh HardDrive: System 9 Folder: Preferences: Textco Preferences
Select this folder and delete by dragging to the trash can - and emptying the contents.
Next, uninstall the GI application.
Simply drag the entire GI application folder to the trash, and empty the contents.
Now, reinstall GI from the original CD - and launch the program with the CD in the drive to verify the license.
2. I read something about "Hotlinking" - what is it, why would I want to use it, and how do I utilize it?
Tutorial 4 found on page 2-18 of the Gene Inspector manual describes Hotlinking in detail. The premise behind "Hotlinking" is that it is often desirable to have the results of an analysis directly connected to the sequence being analyzed - in such a way that if the sequence is changed, the output object is recalculated automatically without you having to remember to do it manually. The sequence might represent one that you are refining in the lab, a multiple aligned consensus sequence, or a contig.
Essentially after running an analysis on a sequence (or group of related sequences) of interest, one can select the analysis output(s) and then choose the menu option, "Notebook > Links > Automatic". You will see the appearance of a small green circular "adorner" icon in the top right corner of each output object indicating that it is now "hotlinked" (See Figure 2.14 in the GI Manual). They should all be green, indicating that no sequences have been changed since the analysis was initially run.
Now supposing that with some additional sequencing you were able to identify additional bases within your sequence of interest. You open the sequence file and type in the newly discovered characters. This changes the sequence and will notify the corresponding output object (the analysis result) in the GI notebook that it needs to be updated.
You'll now notice the change in the hotlink adorner for the analysis that depends on the sequence of interest. The adorner now is red and yellow containing an exclamation point (Figure 2.15 in the GI Manual). Notice that only the analysis object which is dependent on the altered sequence needs to be updated.
Instead of setting up and running a new analysis with the now updated sequence - you’ll simply need to choose the menu option, "Notebook > Links > Perform Auto Recalc Now" ....
Hotlinks can be very useful in saving you time - not only can you utilize the hotlinking feature to keep analysis up to date with minor changes in your target sequence - but you can also create a notebook containing many analyses, all hotlinked to a specific sequence. When you want to perform this set of analyses on any new sequence, just paste in the new sequence in place of the original sequence and then perform the auto recalc.
3. Is there a way to apply a format to text in the GI notebook (similar to the Format Painter in MS Word)?
Yes - Gene Inspector refers to these as "Style Sheets". Tutorial 10, on page 2-34 in the GI Manual explains style sheets in detail.
To create a "Style Sheet", simply select a word of text and change it to the format you desire (font, size, color, etc.). Now you can add this "Style" to the Style Sheet menu for future use by selecting the text, whose style you just changed, and then choosing the menu option, "Format > Style Sheets > Add Style Sheet ...". You'll be presented with a dialog box in which you can name the "Style", then press OK to add the style to the "Format > Style Sheets" menu.
You can apply this "Style" to either blocks of text, or even analysis output objects by simply selecting the target and choosing the menu option, "Format > Style Sheets > (name you gave the style)".
Additionally, Style Sheets can be used to quickly change the look of analysis outputs - simply select the object you want to alter in the output (title, axis label, etc.) and use the Format menu to change fonts, sizes or color combinations. Once you have the graph looking as you like, just select the menu option, "Format > Style Sheets > Add Style Sheet ..." as before. Perhaps you can name the style, "Graph Format" and use this every time a graphing analysis is generated.
4. How can I customize the look of a Multiple Sequence Alignment? I read somewhere that there are 640 ways of displaying MSA’s using Gene Inspector.
In addition to storing and displaying sequences, the sequence editor is the convenient place from which to launch multiple sequence alignments and to fine tune the alignments once they are generated.
Multiple sequence alignments can also be created as a "New Analysis" through the standard analysis setup panel. Beginning on page 2-22, Tutorial 5 in the GI Manual discusses Multiple Sequence Alignments in detail.
After generating a Multiple Sequence Alignment either through the "New Analysis" feature - or simply choosing the menu option, "Sequence > Alignment > Align All Sequences..." from within the Sequence Editor window you have a number of options available:
- Choose Sequence > Display > Hide Overview. This will hide the overview "pane" at the top of the sequence window which is no longer helpful because all sequences being displayed are now the same length.
- Choose Sequence > Consensus > Show Consensus Row. This will add a new row above the sequences showing the consensus sequence - the most common character in that particular position of the alignment.
- Choose Sequence > Consensus > Show Scoring Row. This will add a row containing a histogram indicating how good the match is at each position.
- Finally, choose Sequence > Consensus > Show Shading. This will add shading to the document (shown in Figure 2.19 of the GI Manual). The shading indicates which residues match the consensus sequence residue. The more residues that match the consensus residue, the more intense the shading will be.
Click on the word "SCORE" in the name column to select the entire scoring row. Try choosing different colors and patterns using the Format menu. Notice how the shading changes to reflect your choices.
The most powerful and flexible way to illustrate an MSA is to choose to place "Custom Adornments" on the aligned sequences. Choose Sequence > Consensus > Custom Score Adornments... and try some of the options for depicting the aligned sequences in the exact arrangement you want such as:
- Grade background color of characters that match / or don't match the consensus sequence
- Fill behind characters that match / or don't match the consensus sequence
- Invert the characters that match / or don't match the consensus sequence
- Replace characters that match / or don't match the consensus sequence
- Draw boxes around characters that match / or don't match the consensus sequence
The "Custom Adornments" dialog gives you the ability to preview changes or "Try Out" before committing to a format - giving you the flexibility to customize the MSA display to best "paint your picture" of what is going on.
5. Is there a way to have all analysis outputs of related sequences be displayed in a single output object? I’ve got a group of sequences that I want to look at simultaneously - before deciding what additional analyses will need to be run.
Gene Inspector allows you to run what we call "Summary Analyses" on multiple sequences at once - and present the results in a single summary output object. From this resulting output object it is possible to see more details of any of the individual sequence analyses it contains. Summary Analyses are not available for every analysis offered in Gene Inspector, but rather only for those where this type of display is most appropriate - for example identifying a sequence of nucleotides in a set of related sequences from different organisms.
Within the "Analysis Setup" panel, a check box in the lower right hand corner can be selected to "Show summary results". Add the sequences and run the analysis as normal - the "summary result object" will appear in the notebook window when complete. The object will list all sequences examined, and provides a graphic overview of the analysis to serve as a starting point for further analysis. Without using the "Summary Analysis" option in the setup panel, the results would have been displayed as separate analysis output objects.
Furthermore, you can select any single analysis from the summary and choose the menu option, "Object > Show Info ..." to launch the detailed (single sequence) analysis on the chosen sequence. The results will be seen as a new object in the GI notebook.
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