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CANADA: dsc

dsc - The DNA Sequence Compiler (version 3.09)

The DNA Sequence Compiler is in many aspects similar to dsg, the DNA Sequence Generator.
But this tool is not limited to generating a pool of unrelated sequences. It also pays respect to the concatenation
of sequences, i.e. it also considers nb-tuples overlapping two (or maybe more, if sequences are shorter than
nb) concatenated sequences, when enforcing nb-uniqueness (see the manual for more details on nb-uniqueness.
It also allows for a controlled violation of nb-uniqueness if this should be necessary for a successful sequence
generation.

See the manual for a more detailed description of this tool.
Read the logfile to see what's new in this version.

Download    

The program: dsc.exe (690 KB)
Example input files: dsc_4WJ.dln (1 KB) dsc_DX.dln (1 KB) dsc_RNG.dln (1 KB)
Example config file: dsc_config.cfg (1 KB)

Example

This DeLaNA input file:

SEQUENCETYPE terminal {
  length = 20;
  GC_ratio = 0.5;
}

SEQUENCETYPE variable {
  length = 10;
}

terminal s, e, t0, t1;

variable A;

SEQUENCE HindIII {  // restriction site
    seq_mask = "aagctt";
    }
   
SEQUENCE BamHI {    // restriction site
    seq_mask = "ggatcc";
    }

CONCAT HindIII, s;
CONCAT s, A;

CONCAT A, t0;
CONCAT t0, A;

CONCAT A, t1;
CONCAT t0, A;

CONCAT A, e;
CONCAT e, BamHI;

POOL p {
    N_uniqueness = 4;
    Violation_tolerance = 1;
    Sample_conc = 2e-7;
    Na_conc = 1.0;
    Tm_method = NNSantaLucia;
    }

DESIGNTOOL  {
    Random_Seed = 0;
}

produces the following output:

SEQUENCETYPE terminal {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = [0;100];
    DG = [-1e+010;1e+010];
    seq_mask = "";
}

SEQUENCETYPE variable {
    NA_type = DNA;
    length = 10;
    GC_ratio = [0;1];
    Tm = [0;100];
    DG = [-1e+010;1e+010];
    seq_mask = "";
}

SEQUENCE s {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = 69.6913;
    DG = -24.34;
    seq_mask = "cggtaacaacctaaacgagc";
}

SEQUENCE e {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = 70.2005;
    DG = -24.17;
    seq_mask = "gtatgccccgtcttttctga";
}

SEQUENCE t0 {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = 72.0968;
    DG = -23.97;
    seq_mask = "atcatctccctggaatgggt";
}

SEQUENCE t1 {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = 68.2529;
    DG = -23.64;
    seq_mask = "tagttcactgtagagtccgc";
}

SEQUENCE A {
    NA_type = DNA;
    length = 10;
    GC_ratio = 0.6;
    Tm = 45.4288;
    DG = -12.02;
    seq_mask = "gtggtcgcaa";
}

SEQUENCE HindIII {
    NA_type = DNA;
    length = 6;
    GC_ratio = 0.333333;
    Tm = 1.97983;
    DG = -4.42;
    seq_mask = "aagctt";
}

SEQUENCE BamHI {
    NA_type = DNA;
    length = 6;
    GC_ratio = 0.666667;
    Tm = 1.45266;
    DG = -4.97;
    seq_mask = "ggatcc";
}

POOL p {
    sequences = ;
    n_uniqueness = 4;
    Hamming = 0;
    H_distance = 0;
    Homology = [0;1];
    sample_conc = 2e-007;
    Na_conc = 1;
    formamide_conc = 0;
    Tm_method = NNSantaLucia;
    salt_method = Unified;
    no_shorties = false;
    no_GGG = false;
    no_AUG = false;
    no_GUG = false;
    no_UUG = false;
    no_fraying = false;
    base_strand_GC = [0;1];
}

CONCAT HindIII, s;

CONCAT s, A;

CONCAT A, t0;

CONCAT t0, A;

CONCAT A, t1;

CONCAT t0, A;

CONCAT A, e;

CONCAT e, BamHI;

DESIGNTOOL  {
    Random_Seed = 1174060586;
    ID_in_table = false;
    Analyze_Uniqueness = false;
}
last modification: Apr/17/2009

  
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