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.
- RNAML Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure

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, Uses the first displayed secondary structure annotation.
- Base Pair Conservation Analysis - shown as a histogram and base-pair logo below the alignment. Uses the first displayed secondary structure annotation row.
- 2D Structure Visualization in VARNA - allows linked viewing of the consensus or an individual sequence's structure. Accessed via the Sequence ID popup menu.
- per sequence secondary structure annotation
  Sequence associated secondary structure annotation imported via stockholm, PDB files, or other sources can be shown on the alignment with the Colours→By Annotation dialog box. Colours are assigned according to RNA helix topology number (number of distinct nested helices). Alignments can also be sorted by RNA helix secondary structure topology number, via the Calculations→Sort→By Annotation→Secondary Structure option (only present when per-sequence secondary structure is 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