DNA sequences at a glance

PLoS One. 2013 Nov 21;8(11):e79922. doi: 10.1371/journal.pone.0079922. eCollection 2013.

Abstract

Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(-) and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Fungal
  • Chromosomes, Human
  • DNA / genetics*
  • DNA, Fungal / genetics*
  • Humans
  • Schizosaccharomyces / genetics
  • Sequence Analysis, DNA / methods*
  • Telomere

Substances

  • DNA, Fungal
  • DNA

Grants and funding

Supported by the European Fund for Regional Development (FEDER) through the Operational Program Competitiveness Factors (COMPETE) and by the Portuguese Foundation for Science and Technology (FCT) in the context of projects FCOMP-01-0124-FEDER-010099 (FCT reference PTDC/EIA-EIA/103099/2008) and FCOMP-01-0124-FEDER-022682 (FCT reference PEst-C/EEI/UI0127/2011). SPG acknowledges funding from the European Social Fund and the Portuguese Ministry of Education and Science. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.