ADOPS - Automatic Detection Of Positively Selected Sites

More Information | Back to archive
Full Text of this article Full article [PDF] (1,26 MB)
doi doi:10.2390/biecoll-jib-2012-200
submission July 02, 2012
published July 24, 2012
NCBI PubMed PubMed ID 22829571

David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Cristina P. Vieira, Nuno A. Fonseca and Jorge Vieira

Correspondence should be addressed to:
Jorge Vieira
Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
tp.pu.cmbi@nullarieivbj


Abstract

Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

Reference

David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Cristina P. Vieira, Nuno A. Fonseca and Jorge Vieira. ADOPS - Automatic Detection Of Positively Selected Sites. Journal of Integrative Bioinformatics, 9(3):200, 2012. Online Journal: http://journal.imbio.de/index.php?paper_id=200
imprint | sitemap | credits | top