BMC Bioinformatics, 8(Suppl.2):S10, May 2007.
Trevor I. Dix, David R. Powell,
Lloyd Allison, Julie Bernal,
Samira Jaeger, Linda Stern
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
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.
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
We also show how to highlight
all sets of self-repetition features, in this case
within Plasmodium falciparum chromosome 2.
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.
- Trevor I. Dix, David R. Powell, Lloyd Allison,
Julie Bernal, Samira Jaeger, Linda Stern.
- Comparative analysis of long DNA sequences by per element information content using different contexts.
- BMC Bioinformatics, 8(Suppl 2):S10, May 2007,