3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Nucleic Acid Support</title>
24 <style type="text/css">
27 font-family: "Courier New", Courier, mono;
36 <strong>Nucleic Acid Support</strong>
39 <em>Colour Schemes</em>
41 <p>Jalview has color schemes for nucleic acid based sequences,
42 ability to fetch sequences from RFAM and RNA secondary structure
45 Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
46 colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
47 Purine/Pyrimidine colour scheme</a> are available under the Colour Menu.
48 See <a href="../colourSchemes/index.html">Colour Schemes</a>.
53 Jalview supports annotation of RNA sequences with secondary structure
54 information. You can interactively
55 <a href="../features/annotation.html#rna">create and edit RNA
56 secondary structure annotation rows</a>, or import data in the following
59 <li><em>RFAM</em> - Sequences can be <a
60 href="../features/seqfetch.html">fetched</a> from the RFAM database
61 by accession number or ID.</li>
62 <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
63 notation found in the secondary structure annotation line will be
64 imported as sequence or alignment associated secondary structure
66 <li><em>Clustal files</em> - certain RNA alignment programs, such
67 as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
68 output consensus RNA secondary structure lines in the line normally
69 reserved for the Clustal consensus line in a clustal file.</li>
70 <li><em>RNAML</em> Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li>
73 <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
74 If a sequence or RNA alignment has secondary structure information,
75 the alignment will have a secondary structure line shown below it, and
76 a number of additional options become available:
78 <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
79 Helix colouring</a> - highlights columns of alignment involved in
80 particular RNA helices.</li>
81 <li><a href="../calculations/structureconsensus.html">Base Pair
82 Conservation Analysis</a> - shown as a histogram and base-pair logo
83 below the alignment.</li>
84 <li><a href="../features/varna.html">2D Structure
85 Visualization in VARNA</a> - allows linked viewing of the consensus or
86 an individual sequence's structure</li>
88 <p><strong>Pseudo-knots</strong><br/>
89 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.<br/>
90 Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.</p>
92 <p><strong>Limitations when working with RNA in Jalview</strong><br/>
93 Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
95 <em>Jalview's RNA handling capabilities were introduced in v2.8</em>
97 <p align="center"> </p>