In order to start CE analysis, you have to select the signal and reference channels. By default, the first and the last channels represent the signal and reference, respectively. Depending on the experimental procedure you use, any arbitrary channels can be the signal and reference. In this step, examine the CE profiles shown below and select one signal and one reference channel.
In this step, you are to specify the region of interest (ROI) on your CE profile. HiTRACE will use only the specified ROI in downstream analysis. To facilitate your choice, the signal and reference channel profiles are shown below. Left click, drag, and release, in order to specify the start and end of your ROI. Alternatively, you can let HiTRACE detect your ROI automatically. To do that, simply click the Auto Specification button. In any case, the start and end points of your ROI will be presented in pixel units. Additionally, you can zoom in and out vertically, in order to magnify or reduce the images of CE profiles.
In this step, you can check the intermediate result HiTRACE has processed so far. If you are satisfied with it, you can proceed to the next step for experimental information. Otherwise, you can go back to the previous steps and redo your analysis.
In this step, you setup the experimental information, which are the sequence, the desired structure, the probing region and the type of each capillary. Setting up a experimental information in two phases.
In this step, you can annotate each band locations with a residue. On the image, you can add or remove annotations by clicking a position. You can adjust the brightness and size of the image for fine tuning. HiTRACE-Web also provides a way to perform band annotation in an automated fashion. To use this feature, simply click the "Automated Band Annotation" button.
In addition to the automated band annotation functionality, users are provided with a user-friendly interface to fine-tune band annotation results manually. Red circles represent the residue locations. Each type of nucleotide is associated with a different color (G: green, C: cyan, U: blue, and A: red). By clicking the image, user can (de)select the position of individual residues. The auto-assigned bands are shown on the right side in gray for easier referencing when manually adjusting the assignment.
Now you are done! HiTRACE-Web provides the images of the aligned signal and reference channels. You can also download the peak quantification result. In case you want to redo analysis, you can go back to previous steps.