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