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CANADA: nb_unique

nb_unique (version 1.03)

This program reads a pool of DNA sequences from an input file, analyzes the frequency
of subsequences of a given length, and reports non-unique subsequences to standard
output. 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 may not occur.
nb_unique finds and reports each subsequence of length nb within a given range 
violating this uniqueness property by occuring more than once (complement included)
or being self-complementary. This uniqueness concept is also used in the sequence design
tools.

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:  nb_unique.exe (628 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Example

This tool can take such sequences from a file:

ttcgccctgctactaacacg
agataacagcaggatttctt
ggatcgcaggatctcagtca
gtgaccctccttccagtccg
gaattccatatcccttccaa
agaccgggctccgcacctgt
cttcacatacaaaattaatc
gtccttcccgcggtttctac

and produces a table that starts like this:

Length    Base strand    Frequency    Seq-No    Pos    Sequence    self-comp
4    tcgc    2    0    1    ttcgccctgctactaacacg    no
4    tcgc    2    2    3    ggatcgcaggatctcagtca    no
4    gccc    2    0    3    ttcgccctgctactaacacg    no
4    gggc    2    5    5    agaccgggctccgcacctgt    no
...
last modification: Apr/17/2009

  
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