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Algorithms to compute DNA complexity
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== SeqComplex ==

This is a collection of methods to compute the composition and complexity of a DNA sequence(s) from a Fasta file.

The is a Perl Module containing implementations for each complexity 
measure.  Additionally, several tools are provided which utilitize this module. They include:
(1) compute the methods in a windowed mode.
(2) compute the methods using the whole sequence.
(3) Example script to run all methods in windowed mode and save raw data
                    for later processing.
(4) Example script to read in raw data from and 
                     display as either a table or a Google Charts HTML file.
Computed methods
  *gc: C+G content     
  *gcs: C+G skew
  *cpg: CpG skew
  *cwf: Complexity by Wootton & Federhen
  *ce: Entropy
  *cz: Complexity as compression ratio (using Gzip)
  *cmN: Complexity as Markov model size of N
  *ctN: Trifnov's complexity with order N 
  *clN: Linguistic complexity with order N

Additonal methods
  *ats: A+T skew
  *ket: Keto skew
  *pur: Purine skew

Copyright (C) 2009-2015 by Juan Caballero []

All code is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.8 or, at your option, any later version of Perl 5 you may have available.
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