From 18ec5585c00cf8f8833c30f4dae5c04bc9ecfc65 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 19 Sep 2016 17:43:13 +0100 Subject: [PATCH] JAL-2189 JAL-1369 JAL-192 expand referenceseq documentation --- help/html/calculations/referenceseq.html | 48 ++++++++++++++++++++++-------- 1 file changed, 35 insertions(+), 13 deletions(-) diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html index 03d24a5..912be55 100644 --- a/help/html/calculations/referenceseq.html +++ b/help/html/calculations/referenceseq.html @@ -26,25 +26,47 @@

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. When a reference sequence has been defined, the Format→Show - unconserved option highlights mutations with respect to the - reference sequence, rather than the alignment's consensus sequence. -

+ 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. + introduced in Jalview 2.9, and support for storage and retrieval + of reference sequence views in 2.10.

-- 1.7.10.2