X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Freferenceseq.html;fp=help%2Fhtml%2Fcalculations%2Freferenceseq.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=7c0e3dc6073616707fbacef66c3d7faf34e46267;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git
diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
deleted file mode 100644
index 7c0e3dc..0000000
--- a/help/html/calculations/referenceseq.html
+++ /dev/null
@@ -1,71 +0,0 @@
-
-
-
-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.
-
-