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: +
+ 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:
+
+ 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.
+
+
+ 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
+