Navigate to the Alignment Tab
To align two sequences using pairwise alignment, start by navigating to the “Alignment” tab in the top banner. Select the “Pairwise alignment” button and the alignment modal box will open.
Select you Sequences
In the “Pairwise alignment” modal box you will have the option to select two sequences. To do this, select the “+ Add sequence” button and the file selection will open. You can hold ctrl, select two files to align and the press the select button to choose these files. Note you can also choose the options to enter (paste) a sequence manually or upload a sequence from your local device if the desired file is not present in your “My files”.
Select the Algorithm
Once you have selected your two files you can click the “Next” button. This will take you to the algorithm selection. For pairwise alignment there are two options available, the Local or Smith-Waterman algorithm and the Global or Needleman-Wunsch algorithm. For local pairwise alignment you can also set the parameter by selecting the “(advanced)” button, here you can set the penalties, offset and maximum iterations. Once finished selecting and configuring the alignment algorithm select “Next”.
Saving your Alignment
You will be prompted to name your alignment file. By default the name is set to “Sequence 1 + Sequence 2 etc.”. Then select “Align” this will perform the alignment and save the file to the chosen filename. You will then be taken into the alignment view to visualize the result.
Display Options in Alignment View
Once the alignment is completed, it will be displayed in the alignment view. In the top banner you will notice that the “View” tab options have changed. The first option is the model indicator dropdown, for pairwise alignment it will display Local or Global depending on which algorithm you chose to use. Next is the “Axis” toggle button, this will turn on and off the axis label below the sequences. The next button called “Chromatogram” is only available for sanger trace files (.ab1) as these contain chromatogram data, for other alignments this is disabled. The “Collapse all” and “Expand all” collapses the sequences into compact view where the features and alignment information is hidden. With the “Highlight when” button you can select which regions are highlighted in red in your sequence. By default all regions that are not matching are highlighted however you can select to switch this to only highlight matching regions or to not highlight at all. With the “Highlight color” dropdown you can select which color is used to highlight the matches or mismatches. Lastly the DNA colors button lets you toggle on the base pair colors (A = Green, T = Red, G = Yellow and C = Blue).
Navigation in Alignment View
At the top of the alignment view, you will see the blue minimap of your alignment, additionally you will see a yellow focus window on the map, this can be used to scroll back and forth across your alignment by holding click in the yellow region and moving back and forth. If you would like to view a larger region, use the two handles on the outside of the yellow focus window to expand or decrease the view. Alternatively, you can scroll back and forth with your trackpad by scrolling horizontally with two fingers or if using a traditional mouse by holding down the shift key on your keyboard and using the scroll wheel on the mouse.
For each of the two aligned tracks you will see some alignment information. The name is displayed with a colored arrow on the left side indicating the directionality of the aligned sequence. Under the name the total length of the sequence is displayed. To quickly navigate to the next mismatch you can use the arrow on the right side of the sequence name to jump to the next.
