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MyTaxa specifications

Information


Unique identifier OMICS_04475
Name MyTaxa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Information


Unique identifier OMICS_04475
Name MyTaxa
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for MyTaxa

MyTaxa in pipeline

2016
PMCID: 4990128
PMID: 27487207
DOI: 10.1038/nature19068

[…] 16s fragment obtained during the initial sag screening and confirmed to be identical. as an additional quality control step, all predicted genes from the 19 sags were taxonomically annotated using mytaxa and the taxonomic distributions of adjacent genes in the concatenated assembly (10 gene windows) were inspected for possible contamination. as discussed in , a contaminant genome […]


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MyTaxa in publications

 (5)
PMCID: 5812944
PMID: 29269503
DOI: 10.1128/AEM.02168-17

[…] relatives (), we looked for the presence of genes encoding bacterial virulence factors from these organisms in both effluent and environmental samples. cross-referencing taxonomic annotations from mytaxa and the virulence factor database (see materials and methods), we determined that virulence factor-like genes from manitowoc wwtp effluent were most closely related to those from aeromonas, […]

PMCID: 5150989
PMID: 27941956
DOI: 10.1038/srep38915

[…] which agrees with the concept that accessibility by decomposer organisms is a constraint on biomass decomposition., at the level of species, using classifications provided by the program mytaxa on shotgun dna reads, the most abundant organisms identified in zc4 were rhodothermus marinus (2.5% of reads), thermobispora bispora (2.1%), symbiobacterium thermophilum (1.5%), sphaerobacter […]

PMCID: 4990128
PMID: 27487207
DOI: 10.1038/nature19068

[…] metagenomes (etnp and etsp), were assembled with idba and genes were predicted on contigs longer than 500 bp with metagenemark.hmm. taxonomic classification of metagenomic contigs was performed with mytaxa. nar operons were identified on metagenomic contigs as described below for the sag assemblies., single amplified genomes (sags) were generated from individual bacterial cells, according […]

PMCID: 4678780
PMID: 26602607
DOI: 10.1016/j.gpb.2015.10.003

[…] larger datasets. it has been freely available in the public domain for the last four years, though its citations are low and it does not seem to be gaining enough attention in the scientific field., mytaxa is the latest novel platform for the taxonomic assignment of metagenomic sequences with high accuracy. it has homology-based bioinformatics framework to classify metagenomic and genomic data […]

PMCID: 3979728
PMID: 24714158
DOI: 10.1371/journal.pone.0093827

[…] genes were subsequently searched against a database of all sequenced bacterial and archaeal genomes and their best match was used to infer the phylogenetic origin of contig sequences using the mytaxa scheme developed in our lab (; http://enve-omics.ce.gatech.edu/mytaxa/)., 16s datasets from the lake lanier samples were deposited in the sequence read archive under the same projects […]


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MyTaxa institution(s)
Centre for Bioinformatics and Computational Genomics, and School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA

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