built-in time savings


Often a researcher will be working on a sequence that is constantly being refined. As new information about the sequence comes to light, there is a need to repeat all the analyses based on that sequence. Gene Inspector has the ability to "hotlink" an analysis to a sequence. This means that when a sequence is changed, all dependent analyses can be updated automatically. There is no need to go back and re-define parameters and re-run each analysis again. The program highlights 'outdated' analyses with a yellow circle containing an exclamation point - quickly showing the user that the underlying sequence information has been changed since this analysis was last performed. Users can simply click to 'Perform Auto Recalc Now' from the Notebook menu to update all out of date analyses.

Hotlinks can be very useful - for example a user can create an entire notebook containing many analyses all linked to a single sequence. To perform this set of analyses on a new sequence, just paste the new sequence in place of the original sequence and perform the auto recalc to update.

Built in Time Savings

interactive output objects

Many analysis results produced by the Gene Inspector program are interactive, and allow users to pursue their thought processes as a biologist rather than be constrained by program design. One example of this is a TestCode analysis. This output combines the TestCode result along with an indication of open reading frames (ORFs) and rare codon usage. Taken together, these three analysis results point to the indicated ORF as being a true coding region. As a biologist, one might next want to translate that ORF and examine the peptide. This is easily done by clicking on the ORF arrow with the mouse and translating it directly to a peptide sequence using the "translate" menu option.

Built in Time Savings

Another example of an interactive analysis is the dot matrix analysis. In this output, different colors represent different extents of similarity between the two sequences (in this case red is the most similar and blue the least similar regions above the threshold). To see what the actual sequence alignment looks like for any particular region of the plot, just select the region with the mouse and choose "align selection" from a menu. This will produce a separate window containing an alignment of the two sequence segments selected in the dot plot. There is no need to go back and start the analysis all over again.

Built in Time Savings

This free flow of thought allows you to concentrate on the meaning of the results rather than on how to run the program. This kind of interaction occurs throughout the Gene Inspector to provide you with a comfortable environment in which to store your experimental results and sequence analyses.