X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fna%2Findex.html;h=de2741b08ddb2b9f006d8596d597f359f4ad1abd;hb=dbcbbb61457cb60da170cf99defec797941015b9;hp=366e357f51d0cfe65442eb53d2da0bde3965913c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/na/index.html b/help/html/na/index.html index 366e357..de2741b 100644 --- a/help/html/na/index.html +++ b/help/html/na/index.html @@ -1,22 +1,24 @@ + -->
- 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
+