Kopf
   
LSXI Home Deutsch English
menu-en
     
Molecular Computing
  Home
  Publications
  Downloads
  Links
     
Ls11 Homepage
CANADA: dsg

dsg - The DNA Sequence Generator (version 2.01)

This tool generates pools of nb-unique sequences. A sequence pool is said to be nb-unique, when each
subsequence of length nb that occurs in the pool occurs only once, and its Watson-Crick complement
does not occur at all. As a consequence, self-complementary subsequences of length nb may not occur.

The user can add a lot of other restrictions on the sequences' physical or chemical properties, like melting
temperature, Gibbs free energy, or GC-ratio. It is also possible to restrict the choice of bases at certain
positions or fix complete subsequences, or to forbid the use of user-specified subsequences. See the
description of the DeLaNA input language in the manual for an enumeration of all sequence properties
that can be specified by the user.

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: dsg.exe (452 KB)
Example input files: dsg_small_pool.dln (1 KB) dsg_big_pool.dln (1 KB)

Example

This DeLaNA input file:

SEQUENCE oli1 {
    length = 10;
    }
   
SEQUENCE oli2 {
    length = 20;
    GC_ratio = 0.5;
    }
   
SEQUENCE oli3, oli4 {
    length = 15;
    Tm = [50;55];
    }

POOL mypool {
    n_uniqueness = 6;
    Na_conc = .05;
    sample_conc = 2e-7;
    Formamide_conc = 0;
    forbidden = "ggg";
  }

DESIGNTOOL {
  Random_Seed = 0;
  }

produces this output:

SEQUENCE oli1 {
    NA_type = DNA;
    length = 10;
    GC_ratio = 0.5;
    Tm = 25.2319;
    DG = -7.46638;
    seq_mask = "tgtgtcatcc";
}

SEQUENCE oli2 {
    NA_type = DNA;
    length = 20;
    GC_ratio = 0.5;
    Tm = 54.7326;
    DG = -18.6712;
    seq_mask = "agcagtgactatgcaatggc";
}

SEQUENCE oli3 {
    NA_type = DNA;
    length = 15;
    GC_ratio = 0.666667;
    Tm = 51.2528;
    DG = -15.4488;
    seq_mask = "ctgcaaaggtgcccc";
}

SEQUENCE oli4 {
    NA_type = DNA;
    length = 15;
    GC_ratio = 0.6;
    Tm = 50.2349;
    DG = -15.2088;
    seq_mask = "agctatctgcacgcg";
}

POOL mypool {
    sequences = ;
    n_uniqueness = 6;
    Hamming = 0;
    H_distance = 0;
    Homology = [0;1];
    sample_conc = 2e-007;
    Na_conc = 0.05;
    formamide_conc = 0;
    Tm_method = NNUnified;
    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];
    forbidden = "ggg";
}

DESIGNTOOL  {
    Random_Seed = 1174059522;
    ID_in_table = false;
    Analyze_Uniqueness = false;
}
last modification: Dec/05/2007

  
<webmaster  ls11.cs.tu-dortmund.de>
Die Universität übernimmt keine Haftung für den Inhalt verlinkter externer Internetseiten