From 817fdd1ec02b7666659f96c5ddb34a7b13e8a0e7 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 03:39:03 +0100 Subject: [PATCH] JAL-1645 JAL-1595 sort by RNA helices docs --- help/html/na/index.html | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/help/html/na/index.html b/help/html/na/index.html index 11549fd..e860cf4 100644 --- a/help/html/na/index.html +++ b/help/html/na/index.html @@ -77,14 +77,24 @@ td { + an individual sequence's structure. Accessed via the Sequence ID popup menu. +
  • per sequence secondary structure + annotation
    Sequence associated secondary structure + annotation imported via stockholm, PDB files, or other sources can + be shown on the alignment with the Colours→By + Annotation dialog box. Colours are assigned according to RNA + helix topology number (number of distinct nested helices). + Alignments can also be sorted by RNA helix secondary structure + topology number, via the Calculations→Sort→By + Annotation→Secondary Structure option (only present when + per-sequence secondary structure is available).
    • +

    Pseudo-knots
    Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.
    Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.

    -- 1.7.10.2