Three selection boxes are included at the top-right of the page to customize the display all tabs in the Key Annotation section. The boxes can be used to customize:

• The colour scheme - a selection of well known colour schemes are given
• The numbering scheme
• The CDR region definition

Numbering & Regions

If the query sequence has been numbered, this section displays residue numbers and regions for the default numbering scheme and region definitions. Only the numbered section is displayed. See the Region Sequence Details section for alternative numbering schemes and region definitions. Numbering schemes and region definitions are explained in the help for the About / Definitions page.

The sequence table is divided into fragments to aid viewing. Each fragment has the format.

The first row of the table shows the residues of the sequence of interest. If DNA is available, a protein/DNA alignment will have been attempted, and the aligned codons will also be displayed. The DNA row can be hidden from view by selecting the respective hide icon and viewed again by clicking the 'Show DNA' button.

The next row of the table shows the residues numbers according to the selected numbering scheme. Insertions are highlighted in black.

The next row of the table gives the frequency of occurrence of the residue at the given position, based on the selected numbering scheme.

The next row of the table highlights the CDR (loop) regions in light grey and the framework regions in darker grey.

The symbols shown in the final row indicate Unusual residues (residues occuring in less than 1% of all sequences for a given numbered position). Symbols also indicate potential post-translation modification sites such as N-linked glycosylation sites and phosphorylation sites as well as alerts such as:

• residues in sequences for which a structure was available but where the residue was not resolved in the crystal structure,
• residues in sequences where both a protein and DNA sequence were available but where no codon could be aligned.

A key is shown below the sequence to indicate the meaning of each symbol.

The basic sequence data can be exported to an Excel spreadsheet (XML format) by clicking the 'Export to Excel button'. This will export the residue numbers, residue name and the frequency.

The distribution graph (histogram) is shown indicating the frequency of occurrence of each residue type at the selected position in the sequence (by default this is the first position*). The residue for that position is coloured according to the colouring system selected, all other residues are grey. This graph is supported by an equivalent table indicating the number of sequences in the database in which given residue orrurs at the selected position, and the relative frequency. Again, the selected residue is coloured accordingly.

To change the residue of interest, click the residue number (e.g. 'H23') in the sequence.

The distribution table can be exported to a CSV file by clicking the 'Export frequency tabke to CSV' button.

Humanness

The 'humanness' of your sequence is calculated using the method of Abhinandan and Martin (2007) [J. Mol. Biol 369:852-862].

The graph shows a distribution of scores for expressed human sequences and for expressed mouse sequences. The score for the sequence of interest is indicated by a vertical dashed line.

There are four display options: Heavy, Light, Lambda and Kappa, which can be selected using the respective buttons. In addition, display of the mouse distribution can be switched off using the respective toggle button. The default view is a smoothed graph, but the original data can be viewed by toggling the respective Smoothing button.

Comparison organism

The sequence data are given for all organisms in the database. However, this can be changed by selecting a different organism in the Comparison Organism list.

Threshold

The sequence data are shown for all residues. However, the listing can be reduced by selecting a cutoff Threshold for the frequency. When selected, only residues with a frequency below or equal to this threshold are displayed. (*Note that the distribution graph and table will now be based on the first residue being displayed (i.e. below the threshold).

Accessions & annotations

A summary of computed and textual annotations is provided. This includes chain classification, human subgroup assignment (where appropriate), warnings, identical sequences, data provenance and references.

Tools

The Blast button transfers the protein and/or DNA sequence into the Blast query page where either sequence can be blasted against various sequence sets in the abYsis database.

If there is a DNA sequence but no protein sequence (for example, if no translation was provided by the Data Source) the Translate & Annotate button will appear. This will transfer the DNA to the Key Annotation Query form where abYsis will attempt to translate and annotate it.

Sequences

The protein and/or DNA sequence will be repeated here in a simple text format that can be cut-and-pasted into other software.