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NESTEDALIGN


Sequence and Structure

Dot-parentheses format (also known as dot-bracket format)

Default format. In this format, the sequence is given first. Then, the structure is given, with matching parentheses ( and ) denoting a base pair, and a dot denoting an unpaired base.
Example :





BPseq format

The bpseq format is a simple text format in which there is one line per base in the molecule, listing the the position of the base (leftmost position is 1), the base name (A,C,G,U, or other alphabetical characters), and the position number of the base to which it is paired, with a 0 denoting that the base is unpaired.
For example, the structure represented in dot-parentheses format above would be represented in bpseq format as follows :


N.B.: "Filename", "Organism", "Accession Number" and "Citation and related information available at ?" fields are required.



CT format

The first line contains the sequence length L (which can be followed by the name of the molecule). There are L subsequent lines, one per nucleotide. The ith line starts with i, then the letter denoting the ith nucleotide, then the 5'-connecting base index (i-1), then the 3' connecting base index (i+1), then the paired base index (or 0 if unpaired), and finally base index in the original sequence.
For example, the structure represented in bpseq format above would be represented in ct format as follows :



It's possible to load two different formats for one comparison.


Alignement

Algnment mode options :


Score

NestedAlign has a default "light" score matrix.

But it's possible to choose two other score matrix types :





VARNA


Options

Open

Open from a dot-bracket manual input via 'Open->User input' or 'M' shortcut. Inputs could also be done from a DBN, BPSEQ or CT file with 'Open->file'.



Shortcut keys

Shortcut Description Available with modification off
1
Redraw with radiate algorithm
yes
2
Redraw with circular algorithm
yes
3
Redraw with NAView algorithm
yes
D
Color dash bases (-)
yes
F
Full screen view
yes
M
Manual input
O
Open file
P
Print the RNA
yes
R
Reset the view
yes
S
Color special bases (non A,C,G,U,-)
yes
T
Set title


Script options

Résumé

Param name Value format/type Description Since version
algorithm
String (e.g. "radiate")
Sets the layout algorithm to be used for initial placement. As of version 1.0, valid values for this options are radiate (Tree-like structure) and circular (Circular Feynman's diagrams)
1.0
applyBasesStyle
String
See basesStyle description
3.0
backbone
Color (e.g. #00FF00)
Sets the color used to draw the bonds involved in the backbone
1.0
background
Color (e.g. #8FFF00)
Sets the background color
1.0
baseInner
Color (e.g. #00FFFF)
Sets the color used to fill the disc on top of which the nucleotide is drawn
1.0
baseName
Color (e.g. #F0FF0F)
Sets the color used to draw the nucleotide name
1.0
baseNum
Color (e.g. #FF0000)
Sets the color used to draw the nucleotide number
1.0
baseOutline
Color (e.g. #808080)
Sets the color used to draw the outer circle around the nucleotide
1.0
basesStyle
String
See applyBasesStyle description
3.0
bp
Color (e.g. #60A080)
Sets the color used to draw the base-pairings (hydrogen bonds)
1.0
columns
integer
Sets the number of columns in a multipanel layout
1.0
comparisonMode
boolean
Sets the applet in comparison mode if true. false by default
3.0
error
boolean
Shows varna errors if true. true by default.
3.0
modifiable
boolean
allow the user to modify the arn display if true. true by default.
3.0
periodNum
integer
Sets the numbering period. Nucleotide numbers will be printed for each base whose position is a multiple of the period n. First nucleotide number is always displayed to provide a frame of reference.
1.0
rows
integer
Sets the number of rows in a multipanel layout
1.0
sequenceDBN
String (e.g. "GGAGUCC")
Sets the raw nucleotide sequence for the displayed RNA. Each base must be encoded in a single character. Letters additional to [A,C,G,U] are tolerated
1.0
structureDBN
String (e.g. "((...))")
Sets the secondary structure of the displayed RNA in Dot-Bracket Notation (DBN). Valid structures in DBN format are well-parenthesized words consisting of dots '.', opening '(' and closing ')' parentheses. Dotted positions will be unpaired, whereas matching parenthesized positions will represent base-pairing nucleotides.
1.0
title
String (e.g. "MyRNA")
Sets the title of the displayed RNA. If set to the empty string "", does not display any title, leaving some extra room for the drawings
1.0
titleColor
Color (e.g. #204060)
Sets the color used to display the title
1.0
titleSize
integer
Sets the font size used to display the title
1.0
warning
boolean
Shows varna warnings if true. false by default.
3.0
zoom
double
Sets the zoom in used
3.0
zoomAmount
double
Sets the zoom amount in used
3.0


Bases Style

basesStyle creates a new style for bases, it defines the outline, the innerline, the name and the associate number color via these parameters:
basesOutlineColor, basesInnerColor, basesNameColor, basesNumbersColor.
Examples:

1  <param name="basesStyle0" value="basesOutlineColor=#000000, basesInnerColor=#0000FF, basesNameColor=#00FF00, basesNumbersColor=#FF0000"/> 
2  <param name="basesStyle1" value="basesInnerColor=#0000FF, basesNumbersColor=#FF0000"/> 
3  <param name="basesStyle3" value="basesOutlineColor=#00FF00"/> 


Apply Bases Styles

applyBasesStyle applies an existing bases style on a list of bases (in only one panel in multiple panels case).
The parameter name means: applyBasesStyle[int: basesStyle number]on[int: panel number]
Examples:

1  <param name="applyBasesStyle0on1" value="22, 23, 24, 114, 115, 116" /> 
2  <param name="applyBasesStyle1on1" value="27, 28, 29, 30, 67, 68, 69, 70"/> 
3  <param name="applyBasesStyle0on2" value="10, 11, 12, 46, 47, 48"/> 
4  <param name="applyBasesStyle3on3" value="54, 55, 56, 97, 98, 99"/> 


Demonstration

1  <applet code="applis.VARNA" 
2  codebase="bin" 
3  archive="VARNA31.jar" 
4  width="90%" height="600"> 
5  <param name="rows" value="1" /> 
6  <param name="columns" value="2" /> 
7  <param name="sequenceDBN1" value="CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGAC 
8  GGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUC 
9  UUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCAC 
10  CGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC"/> 
11  <param name="structureDBN1" value="...(((............(((.(((((((..((((.(.(((((......)))))))))))))))))))) 
12  ...........((((((((.((.........((..((((....................))))..)).....(((...(((.((.((.. 
13  ..)))).)))..)))...)).))))..))))..........)))......"/> 
14  <param name="title1" value="1 human ferritin 5'" /> 
15  <param name="warning1" value="true" /> 
16  <param name="background1" value="#FFFFEE" /> 
17  <param name="modifiable1" value="false" /> 
18  <param name="sequenceDBN2" value="CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGG 
19  AACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAAC 
20  UUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC"/> 
21  <param name="structureDBN2" value="..((((........(((((..((((.((((.((.(.(((((......))))))))))))))))((((((.....(((........))).....)))))).. 
22  .....)))))......)))).....((.((....(((..((......))..)))...)).))...."/> 
23  <param name="title2" value="2 mouse ferritin 5'" /> 
24  <param name="warning2" value="false" /> 
25  <param name="background2" value="#FFEEFF" /> 
26  <param name="modifiable2" value="true" /> 
27  <param name="basesStyle0" value="basesInnerColor=#0000FF" /> 
28  <param name="basesStyle1" value="basesInnerColor=#FF9966" /> 
29  <param name="basesStyle2" value="basesInnerColor=#00CCFF" /> 
30  <param name="basesStyle7" value="basesInnerColor=#FF3399" /> 
31  <param name="basesStyle11" value="basesInnerColor=#00FF99" /> 
32  <param name="applyBasesStyle0on2" value="22, 23, 24, 114, 115, 116" /> 
33  <param name="applyBasesStyle1on2" value="27, 28, 29, 30, 67, 68, 69, 70" /> 
34  <param name="applyBasesStyle2on1" value="43, 44, 45, 46, 47, 48, 49, 50" /> 
35  <param name="applyBasesStyle11on1" value="36, 37, 63, 64" /> 
36  <param name="applyBasesStyle7on2" value="39, 40, 61, 62" /> 
37  <param name="applyBasesStyle0on2" value="149, 150, 151" /> 
38  </applet>