Nucleic Acid Support
Jalview has color schemes for nucleic acid based sequences,
ability to fetch sequences from RFAM and RNA secondary structure
Information on the Nucleotide
colour scheme and
Purine/Pyrimidine colour scheme are available under the Colour
Menu. See Colour Schemes.
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
- 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
- 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
- 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:
Helix colouring - highlights columns of alignment involved in
particular RNA helices, Uses the first displayed secondary
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
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).
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