Comparative analysis of long DNA sequences by per element information content using different contexts

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, findi...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Trevor I. Dix, David R. Powell, Lloyd Allison, Julie Bernal, Samira Jaeger, Linda Stern
• Keywords: BMCBI 2007, Compression Model, Dna Sequences, Long Dna Sequences