Getting Started

Quick Search

Just type the name; jones’ into the Quick Search box at the top of the screen to quickly appreciate the power of abYsis.

For this search, abYsis will return an alignment of all public sequences with an author matching the name jones.

Alignment and Table

Alignments are all built from standardised antibody numbering, with CDRs assigned.

If you see where jones occurred in the search you can display other columns. Select Reference from the General dropdown

An extra Reference column will appear and you can see Jones in each set of authors.

Annotation

Each sequence has a Table row with Post Translational Modifications and CDR predictions calculated by abYsis, together with other information that depends on whether the sequences are from public repositories or your proprietary data..

More information is available in the Table’s Drop Down menus. Display extra columns by selecting from the menus;

Hide unwanted columns by selecting this icon;

Heavy and Light Chain Display

Heavy Chains and Light Chains are shown in separate sections.

Where pairing is known between Heavy and Light they can be shown in the same order in respective tables as well as together in the third section

Sort

In abYsis you can sort on any single region you want with the sort region. Click to start region, move mouse to end of selection and then release mouse.

Below the sort is across part of Framework 3 and CDR–H3

To re-sort simply repeat the selection process.

From Multiple Alignment to Detailed Analysis

Once you have decided which sequence to analyse in detail, simply click on the accession code.

Hint! Depending on your computer and mouse setup you should be able to open in a new tab, allowing you to come back to the multiple alignment if required.

You will be taken to a page that has multiple Tabs the first of which is Summary. You are now able to interrogate your selected sequence in more detail. For each residue position you will see the abYsis frequency for that position (organism specific if selected).

The Distribution graph shows frequencies for all 20 amino acids for comparison at that position. To select a different position, click on the residue of interest.

Post Translational Modifications are now shown in position together with other supporting data.

The Humanness graph outlines the score of this antibody sequence against a distribution of human sequences compared against each other and also mouse sequences compared to human. As you can see, this mouse sequence is in the centre of the mouse-human distribution. If you were to humanise this sequence you would expect the red line to migrate to the right overall as it became more human-like.