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.
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.
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.
Algnment mode options :
By default, global alignment.
NestedAlign has a default "light" score matrix.
But it's possible to choose two other score matrix types :
"Light" type matrix choosen by the user. The matrix file contains 12 floating numbers, which are given the ones under the others. Example :
This numbers respectively corresponds to the score for the following operations :
Score for the deletion or the insertion of an unpaired base
Score for the conservation of an unpaired base
Score for the substitution of an unpaired base with an other
Score for the deletion or the insertion base pair
Score for the conservation of a base pair
Score for the substitution of a base in a base pair
Score for the total substitution of a base pair
Score for a pair splitting into two unpaired bases or the fusion of two unpaired bases into a base pair, without substitution
Score for a splitting or a fusion with a base substitution
Score for the scission or the fusion with two bases substitutions
Score for left or right alteration of a pair in an unpaired base or for left or right completion of an unpaired in a base pair, without substitution
Score for the alteration or completion with substitution
"Full" matrix type, choosen by the user.The matrix file is organise in 7 matrix.
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'.
Available with modification off
Redraw with radiate algorithm
Redraw with circular algorithm
Redraw with NAView algorithm
Color dash bases (-)
Full screen view
Print the RNA
Reset the view
Color special bases (non A,C,G,U,-)
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)
Sets the color used to draw the base-pairings (hydrogen bonds)
Sets the number of columns in a multipanel layout
Sets the applet in comparison mode if true. false by default
Shows varna errors if true. true by default.
allow the user to modify the arn display if true. true by default.
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.
Sets the number of rows in a multipanel layout
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
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.
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
Color (e.g. #204060)
Sets the color used to display the title
Sets the font size used to display the title
Shows varna warnings if true. false by default.
Sets the zoom in used
Sets the zoom amount in used
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:
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]