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