From 7a10ed71f58125c4e1c55daff220ac1f3a586abf Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 25 Sep 2012 12:41:47 +0100 Subject: [PATCH] JAL-970 JAL-1052 (comment about JAL-1140) --- help/html/na/index.html | 84 +++++++++++++++++++++++++++++++++-------------- 1 file changed, 59 insertions(+), 25 deletions(-) diff --git a/help/html/na/index.html b/help/html/na/index.html index bad0c92..39f888b 100644 --- a/help/html/na/index.html +++ b/help/html/na/index.html @@ -29,30 +29,64 @@ td { -

Nucleic Acid Support

Colour Schemes

Jalview has color schemes for nucleic acid based sequences, ability to -fetch sequences from RFAM and RNA secondary structure coloring

Information on the Nucleotide -colour scheme and -Purine/Pyrimidine colour scheme are available -under the Colour Menu. See Colour -Schemes.

RNA Support

Sequences can be fetched from the -RFAM database by accession number or ID.

If an RNA alignment is loaded from a Stockholm file with secondary -structure information in WUSS notation, the alignment can be coloured by -the helices in the secondary structure. Helices are determined by the base-pairing -in the secondary structure line. See -RNA Helices Colouring. Below is an example of this type of coloring

Annotation panel shows the presence of RNA helices and WUSS notation from -input file specifying secondary structure.

- - - -

+ Nucleic Acid Support +

+ Colour Schemes +

Jalview has color schemes for nucleic acid based sequences, + ability to fetch sequences from RFAM and RNA secondary structure + coloring

+ Information on the Nucleotide + colour scheme and + Purine/Pyrimidine colour scheme are available under the Colour Menu. + See Colour Schemes. +

+ RNA Support +

+ Jalview supports annotation of RNA sequences with secondary structure + information. You can interactively + create and edit RNA + secondary structure annotation rows, or import data in the following + way: +

RFAM - Sequences can be fetched from the RFAM database + by accession number or ID.
Stockholm files - WUSS (or VIENNA) dot-bracket + notation found in the secondary structure annotation line will be + imported as sequence or alignment associated secondary structure + annotation.
Clustal files - certain RNA alignment programs, such + as LocaRNA + output consensus RNA secondary structure lines in the line normally + reserved for the Clustal consensus line in a clustal file.

+ RNA Secondary Structure Visualization and Analysis
+ If a sequence or RNA alignment has secondary structure information, + the alignment will have a secondary structure line shown below it, and + a number of additional options become available: +

RNA + Helix colouring - highlights columns of alignment involved in + particular RNA helices.
Base Pair + Conservation Analysis - shown as a histogram and base-pair logo + below the alignment.
2D Structure + Visualization in VARNA - allows linked viewing of the consensus or + an individual sequence's structure

Limitations when working with RNA in Jalview
+ Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation +
+ Jalview's RNA handling capabilities were introduced in v2.8 +

-- 1.7.10.2