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.
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+
+ 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:
+
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
+