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:

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