What is the Alignment View?

Overview and details of the alignment viewer.

 Alignment View

This view acts as a tool to visualise all the filtered sequences in the form of a pair-wise alignment. This gives you an idea of which regions in the sequences show most homology while also allowing you to highlight a particular sequence by simply clicking on the label next to it.

AlignmentView photo 1

Based on the molecular type of the query sequence, two possible scenarios are differentiated. In the case of a AA query input, only AA results are shown in the Alignment View. However in the case of a DNA/RNA query input, two tabs are shown, differentiating DNA/RNA results from AA results.

Moreover, by clicking on the label of a sequence, it is possible to copy on clipboard the following three sequence information: ID, Name and Sequence String.



The left column is called “label” and it represents the Description field that we saw earlier as part of List View. The sequence itself is color coded letter by letter for every matching character in consecutive records. For example, all “A”s are green while all “C”s are yellow.

This page presently only displays the first 50 records.


The Heatmap, displayed above the sequences, indicates the frequency of each amino acid per column, by making use of a colour map. Areas with darker colours represent more common areas, whereas areas marked with brighter colours represent less common areas within the result set. The Heatmap serves two main purpose: firstly highlight areas that are more conserved/common over this result set of 50 records and secondly to navigate easier through the alignments of the results.

HubSpot Video