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-
-Reference Sequences
-
-
-
- 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.
-
-