Biomod/2011/UTAustin/Hook'em Hybridizers/CircDesigNA/Help

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Domain Definitions

This input section specifies all DNA domains which are to be designed. Each line of this text describes a separate domain in the syntax:

<ID> <Length> {Position Based Constraints} {-Option1{(arguments)}} {-Option2{(arguments)}} ...

Where
  • ID is an alphanumeric unique identifier of the domain,
  • Length is the domain's length,
  • Position based constraints define restrictions on the sequence of specific bases in a domain, via IUPAC DNA codes (see table below, for RNA, replace 'T' with 'U'),
    CodePermissible Bases
    N no constraints
    R A, G
    Y C, T
    M A, C
    K G, T
    S C, G
    W A, T
    V A, C, G
    H A, C, T
    B C, G, T
    D A, G, T
  • Option1 and Option2, etc, can be any of the following,
    • -seq(Bases, Min, Max): Specifies that the domain must contain at least Min and at most Max of the Bases bases. Bases can be a single base, or it can be multiple bases by separating each base with the '+' sign. Min and Max are in units of bases, but can be input as integer percentages of the entire domain by adding the % character (see below for examples). To remove either the Min or Max constraint, set them to a negative value.
    • -init(Nucleic Acid String): Specifies the sequence to use as an initial value for this domain. This can be used to aid the designer in finding a solution closer to the input seed value. This option cannot be used if the initial value conflicts with other sequence constraints imposed on this domain.
    <bracket>'ed elements are Required fields, and {bracket}'ed elements are Optional. If position based constraints are provided, then the Length field is ignored.


    Example:
    1 8
    2 8 GAANNNNN
    2a 8 GRRNNNNN
    a 4 GACC
    3 10 -seq(A,-1,-1,T,-1,3,G,1,-1,C,2,4)
    4 8 -seq(P,-1,-1,Z,-1,-1)
    5 23 -seq(G+C,45%,55%)
    6 10 -init(GATTACCCTG)

    Translates to:
    Domain '1' is 8bp long and has no constraints. Domain '2' has 3 locked bases (GAA), and the rest is mutable. Domain '2a' constrains its second and third bases to be As or Gs, the rest of its bases are unconstrained, and the first base will be initialized to G. Domain 'a' is locked, and will not be modified by the designer.
    Wrapping a portion of the constraint in square brackets ('[' and ']') flags that the given portion of the domain is mutable. Domain 3 has composition based constraints imposed, with the -seq option, where
    • Any number of A's are allowed (-1 means no lower bound, -1 means no upper bound)
    • Number of T's <= 3 (-1 means no lower bound, 3 is upper bound)
    • Number of G's >= 1 (1 is lower bound, -1 means no upper bound)
    • 2 <= Number of C's <= 4 (2 lower bound, 4 upper bound)
    Additionally, the -seq option also allows one to permit so-called "exotic" bases (denoted P,Z, which are complementary). By default, these bases are set to lower bound 0, upper bound 0 (so they are disallowed). For domain 4 in the example above, the -seq arguments specify that any number of P and Z are allowed, overriding the default behavior of no unnatural bases. Domain 5 specifies that the number of G's plus the number of C's will be between 45% and 55% of the domain's length. Domain 6 uses the -init option to initialize its sequence.

    Molecules Definition

    The input of this box provides the DNA molecules which are present in the solution being designed. Each line of this textual input describes a separate molecule, by listing its component nucleic acid strands.
    • Each strand is an ordered list of domain ID's, separated by whitespace and enclosed by the 5' end '[' and the 3' end '}' characters.
    • Each domain ID is optionally followed by the reverse complement operator, the asterisk '*'
    • Each domain is marked by a hybridization flag, which is either a '.', a '(', or a ')', which is a dot-parenthesis representation of the secondary structure formed by the molecule. In the absence of a hybridization flag, structure-freeness ('.') is assumed.


    Example:
    C1 [3* 2* 1}
    H1A-loop [1* 4*}
    H1A-tail [1*( 5* 6* 4 1)}
    C1_H1A [3* 2* 1(}[1*) 4*}

    Preview Molecule

    The visualization uses the following color key:
    • G (Double line - base immutable)
    • A (Double line - base immutable)
    • T (Double line - base immutable)
    • C (Double line - base immutable)
    • P (Double line - base immutable)
    • Z (Double line - base immutable)
    • -, N (unconstrained)
    • R (see Domain Defs helpfile for specifics)
    • Y (see Domain Defs helpfile for specifics)
    • M (see Domain Defs helpfile for specifics)
    • K (see Domain Defs helpfile for specifics)
    • S (see Domain Defs helpfile for specifics)
    • W (see Domain Defs helpfile for specifics)
    • V (see Domain Defs helpfile for specifics)
    • H (see Domain Defs helpfile for specifics)
    • B (see Domain Defs helpfile for specifics)
    • D (see Domain Defs helpfile for specifics)

    Hotkeys:
    • Shift"+" - Zoom In.
    • "-" - Zoom Out.
    • "w" - Turn on / off "realistic" molecule dynamics. Turn off for figure creation!
    • "d" - Turn on / off line or bubble display.
    • "a" - Turn on / off domain name display.
    • "p" - Turn on / off circular polymer graph display mode.
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