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
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
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.