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
48 Menu. 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"
61 >fetched</a> from the RFAM database 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,
68 href="http://rna.informatik.uni-freiburg.de/LocARNA"
69 >LocaRNA</a> output consensus RNA secondary structure lines in the
70 line normally reserved for the Clustal consensus line in a clustal
72 <li><em>RNAML</em> Jalview can import RNAML files containing
73 sequences and extended secondary structure annotation derived from
77 <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
78 If a sequence or RNA alignment has secondary structure information,
79 the alignment will have a secondary structure line shown below it,
80 and a number of additional options become available:
82 <li><a href="../colourSchemes/rnahelicesColouring.html">RNA
83 Helix colouring</a> - highlights columns of alignment involved in
84 particular RNA helices, Uses the first displayed secondary
85 structure annotation.</li>
86 <li><a href="../calculations/structureconsensus.html">Base
87 Pair Conservation Analysis</a> - shown as a histogram and base-pair
88 logo below the alignment. Uses the first displayed secondary
89 structure annotation row.</li>
90 <li><a href="../features/varna.html">2D Structure
91 Visualization in VARNA</a> - allows linked viewing of the consensus
92 or an individual sequence's structure. Accessed via the Sequence
94 <li><strong>per sequence secondary structure
95 annotation</strong><br /> Sequence associated secondary structure
96 annotation imported via stockholm, PDB files, or other sources can
97 be shown on the alignment with the <strong>Colours→By
98 Annotation</strong> dialog box. Colours are assigned according to RNA
99 helix topology number (number of distinct nested helices).
100 Alignments can also be sorted by RNA helix secondary structure
101 topology number, <em>via</em> the <strong>Calculations→Sort→By
102 Annotation→Secondary Structure</strong> option (only present when
103 per-sequence secondary structure is available).</li>
106 <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced limited
107 support for working with structures including pseudoknots. Where
108 possible, extended WUSS symbols (e.g. different types of
109 parentheses, or upper and lower case letters) are preserved when
110 parsing RNA structure annotation and will be shaded differently when
111 displayed in the structure.<br /> Extended WUSS annotation is also
112 employed to distinguish different base pair interactions obtained
117 <strong>Limitations when working with RNA in Jalview</strong><br />
118 Currently, Jalview is not able to export RNA secondary structure
119 annotation in any format other than Jalview annotation </br> <em>Jalview's
120 RNA handling capabilities were introduced in v2.8</em>
122 <p align="center"> </p>