Reference Sequence Alignment Views

Many alignment analysis tasks concern a query, or reference sequence. For instance, when searching for sequences from other organisms that are similar to a newly sequenced gene, or when searching for structurally similar sequences for use in homology modelling.

What happens when a reference sequence is defined ?

The reference sequence for an alignment is indicated by its ID being shown in bold. In addition:

Defining the reference sequence

Each alignment view can have its own reference sequence.

Reference sequence based alignment visualisation was introduced in Jalview 2.9, and support for storage and retrieval of reference sequence views in 2.10.