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:

- Reference sequence numbering. Instead of column numbers, the alignment ruler shows the reference sequence positions at each column. At each tick mark, either the reference sequence symbol and position is given, or the column number when a gap is present at that position in the reference sequence.
- Format→Show unconserved highlights mutations with respect to the reference sequence, rather than the alignment's consensus sequence.

Defining the reference sequence

Each alignment view can have its own reference sequence.

- Manually assigning a reference sequence
  A sequence can be marked as the reference sequence by right-clicking on its ID to open the popup menu, and selecting the "(Sequence ID)→Mark as Reference" entry.
- Defining a reference when importing annotation
  Jalview automatically assigns a reference sequence when importing analysis results, such as those returned from JPred . A reference sequence can also be assigned via the SET_REF command in an alignment annotation file.

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