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:
+
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
+