title: Comparative analysis of long DNA sequences by per element information content using different contexts.
abstract: BACKGROUND
  Features of a DNA sequence can be found by compressing the sequence under a suitable model; good compression implies low information content. Good DNA compression models consider repetition, differences between repeats, and base distributions. From a linear DNA sequence, a compression model can produce a linear information sequence. Linear space complexity is important when exploring long DNA sequences of the order of millions of bases. Compressing a sequence in isolation will include information on self-repetition. Whereas compressing a sequence Y in the context of another X can find what new information X gives about Y. This paper presents a methodology for performing comparative analysis to find features exposed by such models.
  
  
  RESULTS
  We apply such a model to find features across chromosomes of Cyanidioschyzon merolae. We present a tool that provides useful linear transformations to investigate and save new sequences. Various examples illustrate the methodology, finding features for sequences alone and in different contexts. We also show how to highlight all sets of self-repetition features, in this case within Plasmodium falciparum chromosome 2.
  
  
  CONCLUSIONS
  The methodology finds features that are significant and that biologists confirm. The exploration of long information sequences in linear time and space is fast and the saved results are self documenting.
authors.affiliation: Faculty of Information Technology, Monash University, Clayton, Australia. trevor.dix@infotech.monash.edu.au
authors.forename: Trevor I
authors.initials: TI
authors.lastname: Dix
authors.forename: David R
authors.initials: DR
authors.lastname: Powell
authors.forename: Lloyd
authors.initials: L
authors.lastname: Allison
authors.forename: Julie
authors.initials: J
authors.lastname: Bernal
authors.forename: Samira
authors.initials: S
authors.lastname: Jaeger
authors.forename: Linda
authors.initials: L
authors.lastname: Stern
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods; D007257:Information Theory; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004247:DNA