Alignment tab

The alignment tab shows an alignment of sequences extracted from the database (a set of results from a search) or uploaded by a user. The initial view of this tab will include all sequences (light and/or heavy) that have come from the search or been uploaded. If both light and heavy chains have been submitted, then two separate alignments will be shown.

The display can be toggled between the alignment view and a summary table giving basic annotation of the sequences. You select the summary table by clicking the Process button below an alignment. Consequently the summary table will show only the light chains, or only the heavy chains (depending which button was pressed). Once you have gone to the summary table, you can return to the alignment view by clicking the Display Alignment button at the bottom of the table, but you will only see the sequences that you have selected in that table.

Both the alignment and summary table provide links to the full key annotation for each of the sequences.

Alignment view

The alignment view shows numbered antibody sequences with a key (.........|.........) at the top of the alignment. Hovering over the key will show the residue number.

Below the key and at the bottom of the alignment is a bar indicating the frameworks (green) and CDRs (red) using the Kabat definitions of the regions. (See the help on About / Definitions page for information of region definitions.)

A Consensus sequence is shown at the bottom of the alignment. The consenseus residue is shown in upper case if that residue type is found in greater than 50% of sequences otherwise the residue is in lower case.

Sorting Sequences can be sorted based on sequence similarity using the Sort button. A representative sequences (most similar on average to the other sequences) is selected and placed at the top of the alignment, with the other sequences shown in groups gradually changing from the representative. By default, sorting is performed over the whole sequence, but the region over which the sort is displayed can be changed using the Region slider handles. This, for example, allows a sort to be performed over a particular CDR.

Colours A selection of amino acid colour schemes is available using the colour dropdown. The Dotify checkbox causes residues the same as the residue above in the alignment to be represented by a dot. The Nocolour checkboxes removes the colouring of those residues. This enables one to focus on differences in the sequences.

Deleting sequences Sequences can be selected by checking the box next to each sequence identifier. Once a set of sequences is selected, click the Delete button to remove the sequence(s). A confirmation dialogue will be displayed.

Exporting sequences The aligned sequences can be exported in FASTA format. Select the sequences to be exported (selecting no sequences is the same as selecting them all) and click the Export button. A dialogue will be displayed showing the sequences in FASTA format and these can then be cut-and-pasted into another application.

Processing To switch to the summary table view, select the sequences of interest (selecting no sequences is the same as selecting them all) and click the Process button. The view will change to the summary table.

Summary table view

The summary table view provides a brief summary of key features and annotations of the sequences, allowing a quick comparison. Displayed annotations include CDR assignments and phosphorylation, hydroxylation, glycosylation and amidation sites. Columns of the table are sortable allowing easy comparison of the sequence properties.

The summary table can be exported in either CSV or Excel format by clicking the CSV or Excel buttons at the bottom of the table respectively.