- 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:
-
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
-
+
+ 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:
+
+ 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
+