This program calculates for each gene the ratio of pN/pS (the metagenomic analogy of dN/dS) based on metagenomic read recruitment, however, unlike standard pN/pS calculations, it relies on codons rather than nucleotides for accurate estimations of synonimity.
What is the pN/pS ratio?
The pN/pS ratio (first described in Schloissnig et al. 2012) is the ratio of 2 rates: the rates of non-synonymous (pN) and synonymous (pS) polymorphism. It is analogous to dN/dS, which is the ratio of rates between non-synonymous (dN) and synonymous substitutions between 2 strains/species. We calculate pN/pS from allele frequency obtained through SCVs and SAAVs (see publication in preparation) for exact implementation details.
Neat. How do I use this program?
Firstly, you’ll need to run anvi-gen-variability-profile twice with the same parameters on the
same databases. The first time, use the flag
--engine AA to get a variability-profile-txt for
SAAVs (single amino acid variants), which we’ll name the
SAAVs.txt in this example. The second
time, use the flag
--engine CDN to get a variability-profile-txt for SCVs (single codon
variants), which we’ll name
SCVs.txt in this example.
Then you can run this program like so:
anvi-script-calculate-pn-ps-ratio -a SAAVs.txt \ -b SCVs.txt \ -c contigs-db \ -o output_dir
This will result in a directory called
output_dir that contains several tables that describe each of your genes. See pn-ps-data for more information.
By default, this program ignores some of the genes and variable positions in your variability profiles; you can choose to be more sensitive or ignore more positions by changing any of these three variables:
- The minimum departure from consensus for a variable position (default: 0.10).
- The minimum number of SCVs in a gene (default: 4).
- The minimum coverage at a variable position (default: 30)
Edit this file to update this information.
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the
__resources__ tag in this file to see an example.