Julio Rozas on Software for DNA Polymorphism Analyses

Emerging Research Fronts Commentary, December 2011

Julio Rozas

Article: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data


Authors: Librado, P;Rozas, J
Journal: BIOINFORMATICS, 25 (11): 1451-1452, JUN 1 2009
Addresses: Univ Barcelona, Fac Biol, Dept Genet, Diagonal 645, E-08028 Barcelona, Spain.
Univ Barcelona, Fac Biol, Dept Genet, E-08028 Barcelona, Spain.
Univ Barcelona, Inst Recerca Biodiversitat, E-08028 Barcelona, Spain.

Julio Rozas talks with ScienceWatch.com and answers a few questions about this month's Emerging Research Front paper in the field of Computer Science.


SW: Why do you think your paper is highly cited?

The new high-throughput DNA sequencing technologies are allowing the identification of millions of SNPs (Single Nucleotide Polymorphisms), including those from non-model species, at an increasingly lower cost. This huge data can be only analyzed using powerful computer programs, such as DnaSP (DNA Sequence Polymorphism).

DnaSP is a multi-purpose program, and one of the first software developed to analyze this data (the first version was launched in 1994); currently it is one of the most popular software to conduct DNA polymorphism analyses.

SW: Does it describe a new discovery, methodology, or synthesis of knowledge?

The paper describes version 5 of DnaSP. In this new version we have implemented many population genetics analytical methods that are useful for analyzing and interpreting DNA polymorphism data. Some of the implemented methods were developed by us.

SW: Would you summarize the significance of your paper in layman's terms?

Lead author: Pablo Librado.
Co-Author: Pablo Librado.

DnaSP software allows users to conduct many of the state-of-the-art analyses of DNA polymorphism data to understand the evolutionary forces underlying nucleotide variation. In particular, the software allows users to estimate the level and pattern of nucleotide diversity within and among populations, recombination rates, the extent of linkage disequilibrium between polymorphic sites, or conducting coalescent-based neutrality tests.

These methods are useful, for instance, to determine the relative role of the different evolutionary forces in shaping nucleotide variation, and hence in detecting the past action of natural selection at the molecular level.

SW: How did you become involved in this research, and how would you describe the particular challenges, setbacks, and successes that you've encountered along the way?

Our team has focused on the DNA polymorphism analysis for years. I became involved during my Ph.D. studies—first analyzing Restriction Fragment Length Polymorphisms (RFLPs), and later DNA sequence polymorphisms. In 1994, I started the development of DnaSP software mainly because at that time there was no software to conduct such analyses. Since that things have changed drastically: from the analysis of a single gene in few individuals to the comparative analysis of several complete genomes.

SW: Where do you see your research leading in the future?

The high-throughput DNA sequencing technologies will enable the DNA sequencing of several complete genomes but at a substantially lower cost. This will certainly require new tools and methods to handle and analyze this new data.

SW: Do you foresee any social or political implications for your research?

The software provides an easy-to-use tool to analyze data and, therefore, has no straightforward social or political implications; but can it have them indirectly, for example, in the analysis of disease-associated DNA polymorphisms.End

Julio Rozas
Professor of Genetics
Universitat de Barcelona
Barcelona, Spain
Web

Pablo Librado
Ph.D. student
Universitat de Barcelona
Barcelona, Spain

KEYWORDS: DNASP V5, SOFTWARE, COMPREHENSIVE ANALYSIS, DNA POLYMORPHISM DATA, POPULATION GENOTYPE DATA, HAPLOTYPE RECONSTRUCTION, STATISTICAL METHOD, SEQUENCE, COALESCENT, CHARACTERS, VARISCAN, GENOMICS.

 
 

   |   BACK TO TOP