J Integr Bioinform - ADOPS--Automatic Detection Of Positively Selected Sites.

Tópicos

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Resumo

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.

Resumo Limpo

maximumlikelihood method base model codon substitut wide use infer posit select amino acid site respons adapt chang nevertheless order use approach softwar applic requir align protein dna sequenc infer phylogenet tree run maximumlikelihood model therefor signific effort made order prepar input file differ softwar applic analysi output everi analysi paper present adop automat detect posit select site softwar develop goal provid automat flexibl tool detect posit select site given set unalign nucleotid sequenc data exampl use pipelin given show differ condit posit select amino acid site set coffea putat srnase sequenc adop softwar freeli avail can download httpsingeiuvigoesadop

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