MLgsc: A Maximum-Likelihood General Sequence Classifier

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 decis...

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Bibliographic Details
Published in:PloS one 2015-07, Vol.10 (7), p.e0129384-e0129384
Main Authors: Junier, Thomas, Hervé, Vincent, Wunderlin, Tina, Junier, Pilar
Format: Article
Language:English
Subjects:
Amino acids
Bioinformatics
Classification
Computer programs
Computer Science
Databases, Genetic
Databases, Protein
Firmicutes
Freeware
Gene sequencing
Genes
Laboratories
Likelihood Functions
Methods
NifH gene
Nitrogenase
Nucleotide sequence
Nucleotides - chemistry
Phylogenetics
Phylogeny
Pipelines
Proteins
Proteins - chemistry
Queries
rRNA 16S
Software
Source code
UNIX
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Description
Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0129384