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ALDEx2 uses compositional data analysis and can be applied to RNAseq, 16S rRNA gene sequencing, metagenomic sequencing, and selective growth experiments. Alexa-Seq is a pipeline that makes possible to perform gene expression analysis, transcript specific expression analysis, exon junction expression and quantitative alternative analysis. Allows ...
The genes coding for it are referred to as 16S rRNA genes and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. [2] Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. [ 3 ]
By using oligonucleotide primers targeted to conserved regions in the 16S and 23S genes, RISA fragments can be generated from most of the dominant bacteria in an environmental sample. While the majority of the rRNA operon serves a structural function, portions of the 16S-23S intergenic region can encode tRNAs depending on the bacterial species ...
In order to assess how many genomes are available, PICRUSt optionally allows users to calculate a Nearest Sequenced Taxon Index (NSTI) for their samples. This index reflects the average phylogenetic distance between each 16S rRNA gene sequence in their sample, and a 16S rRNA gene sequence from a fully sequenced genome. In general, the lower the ...
In bacteria and archaea, there is a single ITS, located between the 16S and 23S rRNA genes. Conversely, there are two ITSs in eukaryotes: ITS1 is located between 18S and 5.8S rRNA genes, while ITS2 is between 5.8S and 28S (in opisthokonts, or 25S in plants) rRNA genes. ITS1 corresponds to the ITS in bacteria and archaea, while ITS2 originated ...
Software for analysis of 16S rRNA gene amplicon sequence data Linux, macOS, Windows: GPL: University of Michigan: Nextflow: A workflow management system used for building and running scalable and reproducible bioinformatics pipelines, especially in cloud and high-performance computing environments. Linux, macOS, Windows: Apache License 2.0 ...
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