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, the table shows the Data Source, the abYsis Accession (linked for further details) and an alignment Score.

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 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 Translate Targets checkbox provides 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.

Advanced Options

Click the Show Advanced Options button to display advanced options.

Select target germline sequences by organism and data source allows you to control the target germline sequences to search. You may specify the Organism, Data Source, Gene Segment and exclude target sequences that have Warnings.

Annotation settings allows the Numbering Scheme to be selected. This has no effect on the search or alignment results. See the About / Definitions page for information on numbering schemes.

Alignment settings allows you to Rank alignments with targets by Alignment Score (the default) or by Identity. You can also Specify the Number of alignments to show - i.e. the number of germline hits to show and whether 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.

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.