Germline View

This tab shows alignments of the query sequence to the most similar similar V, D and J germline gene segments in abYsis. The underlying searches are always performed using the protein sequence as the query with the germline DNA sequences as targets.

The first two rows of the results table shows the query protein sequence together with its aligned codons (where available) and the abYsis numbering (if the sequence is numbered).

The aligned germline sequences are then shown, one per line.

For each germline sequence, hovering over the accession label will reveal the Data Source, the abYsis Accession (linked for further details), an alignment Score, the Identities, and the sequence Length.

Click the Score to obtain a pop-up view of the underlying alignment.

The Identities column shows the total number of nucleotide and/or amino acid matches between the query and the aligned germline DNA sequence. Where query codons are known, we count 1 for each nucleotide match. Where query codons are not known we count 1 for each amino acid match. The second number in the Identities column is the maximum possible number of identities over the aligned region, counted in this way. In default mode, the targets are ranked in order of decreasing identity.

Controls

The Organism selection box allows the organism to be selected. The default is 'Not specified', but this can be set to 'Homo sapiens' or 'Mus' if required.

You can also Specify the Number of alignments to show - i.e. the number of germline hits to be displayed.

The Alignment Focus dropdown at the top of the page allows the alignment view to be focused on particular segments (V, D or J), junction regions (V-J or V-D-J) or an overview showing the whole sequence at once.

The Toggle Targets button toggles display of a translation of each germline DNA sequence according to the reading frame implied by the alignment. Checking this box has no effect on the way the search is performed or the results/ranking.

The Full Width button allows the sequence to be toggled between in single fragment view and the default multi-fragment view.

Advanced Options

Click the button to display advanced options.

The Data Source section allows you to control the target germline sequences to search. You may specify the Data Source, Gene Segment and exclude target sequences that have Warnings.

Alignment settings allows you to Rank alignments with targets by Alignment Score (the default) or by Identity. You can also Specify whether or not to Exclude identical hits - i.e. germline sequences with identical sequences - in the results set.

Search settings allows the scoring thresholds for alignment with different gene segments to be specified.

Distribution graph and table

The distribution graph and table are displayed as indicated in the Summary tab section.

Methods

The V segments are searched first, then the J segments. If V and J hits are obtained and the chain is a heavy chain, the short region between the top hitting V and J aligned regions is excised and used to make a final exhaustive search of the short D segment sequences. Search thresholds may be adjusted using the Search Settings dropdowns.

abYsis uses the exonerate suite of programs [Slater and Birney (2005) BMC Bioinformatics 6:31] for underlying Protein/DNA sequence comparisons.