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MLgsc: A Maximum-Likelihood General Sequence Classifier
Résumé We present software package for classifying protein or nucleotide sequences to user-specified sets of reference sequences. The software trains a model using a multiple sequence alignment and a phylogenetic tree, both supplied by the user. The latter is used to guide model construction and as a decision tree to speed up the classification process. The software was evaluated on all the 16S rRNA gene sequences of the reference dataset found in the GreenGenes database. On this dataset, the software was shown to achieve an error rate of around 1% at genus level. Examples of applications based on the nitrogenase subunit NifH gene and a protein-coding gene found in endospore-forming Firmicutes is also presented. The programs in the package have a simple, straightforward command-line interface for the Unix shell, and are free and open-source. The package has minimal dependencies and thus can be easily integrated in command-line based classification pipelines.
   
Mots-clés Databases, Genetic, Databases, Protein, *Likelihood Functions, Nucleotides/chemistry, *Phylogeny, Proteins/chemistry, Software
   
Citation Junier, T., Herve, V., Wunderlin, T., & Junier, P. (2015). MLgsc: A Maximum-Likelihood General Sequence Classifier. PLoS One, 10(7).
   
Type Article de périodique (Anglais)
Date de publication 2015
Nom du périodique PLoS One
Volume 10
Numéro 7