Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

摘要

The Tax4Fun workflow. 16S rRNA gene sequences are initially aligned against the reference sequences provided with Tax4Fun2 to identify the nearest neighbour. If user-defined data is supplied, the 16S rRNA gene sequences are additionally aligned against the sequences added by the user. Nearest neighbours in the user data will be preferred if both search attempts result in significant hits. The OTU abundances for each sample are summarized based on the results from the nearest neighbour search. An association matrix (AM) containing the functional profiles of those references identified in the 16S rRNA search is generated. The summarized abundances and the functional profiles stored in the AM are merged and a metagenome is predicted for each sample. FTU and FSU values are provided as a log file. To include user data and generate a habitat-specific data set, Tax4Fun2 provides functions to functionally annotate prokaryotic genomes and to extract 16S rRNA gene sequences. User-defined reference data sets are subsequently generated and can be included in the prediction. If large amounts of genomes are provided, extracted 16S rRNA gene sequences can be optionally clustered using the uclust algorithm