Tax4Fun

[…] Tool (BLAST) [] to identify likely representative bacterial species. A rarefied OTU table with the associated centroid sequences is available in . Bacterial functional capabilities were imputed using Tax4Fun [], an algorithm using phylogenetic relationships to predict gene content, ultimately assigning functional pathways using the Kyoto Encyclopedia of Genes and Genomes [,]. […]

[…] is is related to the difference in 16S rRNA gene copy numbers between species, yet this also accounts for other (marker) genes [, ]. Normalization of the 16S rRNA gene copy number was applied for the Tax4Fun analysis, as this is inherent to this software package []. However, no additional normalization to the copy number was applied, given the high variation in 16S rRNA gene copy number between sp […]

[…] o as the taxa-function relationship [], has many practical applications in the analysis of microbial communities. For example, this relationship is explicitly utilized by tools such as PICRUSt [] and Tax4Fun [] for predicting overall community gene content based on the community taxonomic profile and available reference genomes. Other studies have similarly used the taxa-function relationship to i […]

[…] atabase, and Piphillin [], which has implemented an inference tool that works with any current genome database and has improved correlation and accuracy for clinical samples compared with PICRUSt and Tax4Fun [].Metagenomics is one of the most powerful tools available to unravel the complexity of gut microbiota. The integration of metagenomic data and other “omic” techniques (e.g., proteomics, meta […]

[…] re defined by a Venn-diagram analysis using the software available at http://bioinformatics.psb.ugent.be.The OTU table was also used to predict the functional potential of bacterial communities using Tax4Fun []. Since Tax4Fun only recognized taxonomical data from the SILVA database, the OTUs previously obtained (as described in the paragraph ‘Metagenomic DNA extraction and metaphylogenomic analysi […]

[…] prediction of functional profiles of the bacterial community based on our 16S rRNA gene sequences, data from each treatment and the control were run through the newly developed open-source R package Tax4Fun (Aßhauer et al., ) after being processed with Qiime (based on SILVA). […]