DOMINO, a new bioinformatics app to ease studies of genetic diversity through the genome
| Published by University of Barcelona
New bioinformatics tool to develop molecule markers à la carte out of genomic data
Designing techniques to explore genetic diversity through new molecular markers is a constant challenge for the progress in phylogenetic research, and in particular, to study the genomic variation in organisms which are not considered classic models of study. The study of the complete genome at a big scale is opening new perspectives on the biological complexity of organisms, and it responds to an authentic methodological revolution to integrate a great volume of data in lots of scientific disciplines.
Easing the identification and selection of molecular markers distributed throughout the genome of model and non-model organisms is one of the main applications of DOMINO (Development of Molecular markers in Non-model Organisms), an innovative bioinformatics tool presented in an article in the journal Bioinformatics, Oxford University Press, signed by the experts Julio Rozas, Cristina Frías, José Francisco Sánchez, Sara Guirao and Alejandro Sánchez, from the Department of Genetics, Microbiology and Statistics and the Biodiversity Research Institute of the University of Barcelona (IRBio), and Elisa Mora and Miquel A. Arnedo, from the Department of Evolutionary Biology, Ecology and Environmental Sciences and the IRBio.
Overcoming frontiers in the study of the genome at a big scale
"Having the chance to identify new markers or selecting the most suitable ones among a group of existing markers is a previous step in the scientific work of lots of researchers, such as in studies of molecular phylogenomics or phylogeography that use DNA sequencing big data (known as NGS data or next generation sequencing). Actually, it is less common nowadays to have lots of molecular markers in lots of researches", says professor Julio Rozas, who leads the Evolutionary Genomics and Bioinformatics research group at the University of Barcelona (UB) and represents the UB in the Bioinformatics Barcelona (BIB).
"DOMINO is a very useful bioinformatics app for researchers who use both model and non-model organisms" says Rozas. "However, the non-model organisms show more difficulties for the development of molecular markers, because their genomic sequencing is not known so it is difficult to have enough markers of this type".
DOMINO: from molecular phylogenics and phylogenomics to genome population
Compared to other computer software, DOMINO mixes a high flexibility -it allows the use of software with a big diversity of NGS data- with the easy use of GUI (Graphic User Interface) so that the software is used by researchers without bioinformatic knowledge. DOMINO is a computer tool of interest to promote researches in the fields of molecular phylogenetic and genome studies (study of the evolutionary relations of several close species), phylogeography (demographical and selection factors responsible for the current distribution of the species), and in genetics and genomics of the populations (defining genes and genomic areas affected by different evolutionary mechanisms, including demographic and selection processes).
The scientific work to develop DOMINO, coordinated by professors Julio Rozas, Miquel Àngel Arnedo and Alejandro Sánchez-Gracia, shows once more the need for the development of versatile bioinfomatic apps that can be adapted to high speed of progress of the DNA sequencing technologies and their application in evolutionary studies.
"In the future, we expect DOMINO to use NGS data from new technologies -it currently uses DNA sequences from platforms such as 454 or Illumina- apart from working with information given by new experimental apps, resulting from the called RADseq or other strategies based on sequencing of a representative part of the genome" says Julio Rozas, first author of another article published in 2003 in the journal Bioinformatics, about a powerful bioinformatics software to analyze DNA polymorphisms, the most cited work in Spain -1.815 citations- between 1999 and 2009, according to data from Essential Science Indicators.