anvi-get-codon-usage-bias

Get codon usage bias (CUB) statistics of genes and functions..

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contigs-db profile-db collection bin internal-genomes external-genomes

Can provide

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program calculates codon usage bias (CUB) among genes or functions.

A range of options allows control over the CUB calculation to remove statistically spurious results.

Some CUB metrics depend on a reference codon composition while others are reference-independent. The reference often constitutes expected high-expression genes, such as ribosomal proteins. This program allows customization of the reference. It also introduces an “omnibias” mode, in which reference compositions are determined from every gene (or function), and CUB is calculated for every combination of query and reference gene. This produces a square distance-like matrix of CUB values that can be used to cluster genes or functions by their biases relative to one another.

Basic commands

CUB of genes

This command produces a table of CUB values from coding sequences in the contigs database. The first column of the table contains gene caller IDs and each subsequent column contains values for a CUB metric, e.g., the Codon Adaptation Index (CAI) of Sharp and Li, 1987 and 𝛿 of Ran and Higgs, 2012. CUB metrics that rely upon a reference codon composition, such as CAI and 𝛿, establish this composition from genes in the genome that are annotated as ribosomal proteins by KEGG KOfams/BRITE. Certain parameters have default values to increase the statistical significance of results (--query-min-analyzed-codons, --reference-exclude-amino-acid-count, --reference-min-analyzed-codons).

CUB of functions

This command produces a table of CUB values for functions rather than genes. By using --function-sources without any arguments, the output will include every functions source available in a given contigs-db, e.g., KOfam, KEGG_BRITE, Pfam (you can always see the complete list of functions in your contigs-db by running the program anvi-db-info on it). The first four columns of the table before CUB values contain, respectively, gene caller IDs, function sources, accessions, and names.

Custom CUB reference gene set

This command establishes a CUB reference codon composition from genes with functional annotations defined a supplemental file. This file should be headerless, tab-delimited, and have three columns of function annotation sources (required), function accessions, and function names (either an accession or name is required).

“Omnibias” CUB

In reference-dependent CUB metrics, genes or functions are compared to a reference codon composition, such as from ribosomal proteins. “Omnibias” mode compares each gene/function “query” not to a single reference, but to each other gene/function. This generates a square distance-like matrix of CUB values that can be used to cluster genes/functions by their biases relative to one another. The output path given in the command is modified to create an output file of the omnibias matrix for each CUB metric.

CUB from multiple internal and external genomes

This command produces a CUB table per genome, modifying the output path given in the command to create a separate output file per genome. Collection of genomes can be provided as internal-genomes, external-genomes, or both:

Option examples

The following tables show the options to get the requested results.

Selecting CUB metrics and references

Get	Options
With certain, rather than all, CUB metrics	--metrics cai
With query sequences also used as references	--omnibias
With a custom reference defined by functional annotations	--select-reference-functions-txt path/to/select_reference_functions.txt
With a custom reference defined by certain genes	--reference-gene-caller-ids 0 2 500

CUB from sets of genes with shared functions

Get	Options
All function annotation sources	--function-sources
All KEGG BRITE categories	--function-sources KEGG_BRITE
All KEGG KOfams and all Pfams	--function-sources KOfam Pfam
Certain KEGG BRITE categories	--function-sources KEGG_BRITE --function-names Ribosome Ribosome>>>Ribosomal proteins
Certain KEGG KOfam accessions	--function-sources KOfam --function-accessions K00001 K00002
Certain BRITE categories and KOfam accessions	--select-functions-txt path/to/select_functions.txt

CUB from selections of genes

Get	Options
From contigs database	--contigs-db path/to/contigs.db
From collection of internal genomes	--contigs-db path/to/contigs.db --profile-db path/to/profile.db --collection-name my_bins
From internal genome	--contigs-db path/to/contigs.db --profile-db path/to/profile.db --collection-name my_bins --bin-id my_bin
From internal genomes listed in a file	--internal-genomes path/to/genomes.txt
From external genomes (contigs databases) listed in a file	--external-genomes path/to/genomes.txt
With certain gene IDs	--gene-caller-ids 0 2 500
With certain gene IDs or genes annotated with certain KOfams	--gene-caller-ids 0 2 500 --function-sources KOfam --function-accessions K00001

Filtering genes and codons in analyzed and reported queries

Get	Options
Exclude genes shorter than 300 codons from queries	--gene-min-codons 300
Exclude genes shorter than 300 codons from contributing to function queries	--gene-min-codons 300 --function-sources
Exclude function queries with <300 codons	--function-min-codons 300
Exclude stop codons and single-codon amino acids	--exclude-amino-acids STP Met Trp
Exclude codons for amino acids with <5 codons in >90% of genes	--pansequence-min-amino-acids 5 0.9
Replace codons for amino acids with <5 codons in the gene or function with NaN	--sequence-min-amino-acids 5
Exclude queries with <300 codons involved in the CUB calculation	--query-min-analyzed-codons 300

Filtering genes and codons in analyzed references

Get	Options
Codons with a frequency <20 are excluded from the reference and CUB calculation	--reference-exclude-amino-acid-count 20
Exclude references with <300 codons involved in the CUB calculation	--reference-min-analyzed-codons 300

Option details

Functions

Functions and function annotation sources (e.g., ‘KOfam’, ‘Pfam’) can be provided to calculate CUB for functions rather than genes.

Inputs

There are multiple options to define which functions and sources should be used as CUB queries. --functions-sources without arguments uses all available sources that had been used to annotate genes.

--function-accessions and --function-names select functions from a single provided source. The following example uses both options to select COG functions.

To use different functions from different sources, a tab-delimited file can be provided to functions-txt. This headerless file must have three columns, for source, accession, and name of functions, respectively, with an entry in each row for source.

By default, selected function accessions or names do not need to be present in input genomes; the program will query any selected function accessions or names that annotated genes. This behavior can be changed using the flag, --expect-functions, so that the program will throw an error when any of the selected accessions or names are absent.

BRITE hierarchies

Genes are classified in KEGG BRITE functional hierarchies by anvi-run-kegg-kofams. For example, a bacterial SSU ribosomal protein is classified in a hierarchy of ribosomal genes, Ribosome>>>Ribosomal proteins>>>Bacteria>>>Small subunit. CUB can be calculated for function queries at each level of the hierarchy, from the most general, those genes in the Ribosome, to the most specific – in the example, those genes in Ribosome>>>Ribosomal proteins>>>Bacteria>>>Small subunit. Therefore, the following command returns CUB values for each annotated hierarchy level – in the example, the output would include four rows for the genes in each level from Ribosome to Small subunit.

Custom reference

A custom reference codon composition for reference-dependent CUB calculations can be defined by functional annotations and/or genes IDs. By default, the reference codon composition is defined by the concatenation of all genes in the genome annotated as ribosomal proteins by KEGG KOfams/BRITE.

Reference functions

Use --select-reference-functions-txt to provide a table of functional annotations defining a custom set of reference genes. The tab-delimited file should not have a header, but should have three columns of 1) function annotation sources, such as ‘KEGG_BRITE’, ‘KOfam’, or ‘Pfam’, 2) function accession, such as ‘K00001’ for KOfam, and 3) function name, such as ‘Ribosome»>Ribosomal proteins’ for KEGG_BRITE. Every row must contain a source and either a function accession or name.

Require all functions be present

Use --expect-functions to require that all functions that define the reference are found in the genome, else an error will be thrown. By default, not all provided functions need to be represented among the reference genes.

Reference genes

Use --reference-gene-caller-ids for select genes to be in the custom reference gene set. This only works when processing a single genome. An error will be thrown if not all of the provided gene caller IDs are present in the genome.

Filter genes and codons

Codons

It may be useful to restrict codons in the analysis to those encoding certain amino acids. Stop codons are excluded by default from CUB calculations. Codons encoding a single amino acid (Met and Trp) do not factor into CUB calculations. Example: exclude Ala, Arg, and stop codons with --exclude-amino-acids Ala Arg STP.

Dynamic exclusion of amino acids can be useful in CUB calculations. For example, a query gene with 1 AAT and 1 AAC encoding Asn, or “synonymous relative frequencies” of 0.5 AAT and 0.5 AAC, has very little data to support comparison to the synonymous relative frequencies of a large number of Asn codons in a set of reference genes. A query with 1 AAT and 0 AAC, or synonymous relative frequencies of 1.0 AAT and 0.0 AAC, would be even more statistically insignificant. Reference-dependent CUB metrics, such as 𝛿, rely upon the ratio of synonymous relative codon frequencies in the query and reference, and so can be skewed for queries with small counts of various codons. --pansequence-min-amino-acids removes rarer amino acids across the dataset, setting a minimum number of codons in a minimum number of genes to retain the amino acid. For example, amino acids with <5 codons in >90% of genes will be excluded from the analysis with the arguments, --pansequence-min-amino-acids 5 0.9.

Codons for rarer amino acids within each gene or function query can be excluded from the CUB calculation with --sequence-min-amino-acids. For example, amino acids with <5 codons in a query will be excluded from the analysis with --sequence-min-amino-acids 5.

Gene length and codon count

Genes with fewer than a minimum number of codons can be ignored in the CUB analysis. --gene-min-codons sets the minimum number of codons required in a gene, and this filter can be applied before and/or after the removal of rarer codons. Applied before, --gene-min-codons filters genes by length; applied after, it filters genes by codons remaining after removing rarer codons. --min-codon-filter can take three possible arguments: length, remaining, or, by default when codons are removed, both, which applies the --gene-min-codons filter both before and after codon removal.

It may seem redundant for remaining and both to both be possibilities, but this is due to the possibility of dynamic amino acid exclusion using --pansequence-min-amino-acids. Amino acids are removed based on their frequency in a proportion of genes, so removing shorter genes by length before removing amino acids can affect which amino acids are dynamically excluded.

Get	Options
Exclude genes shorter than 300 codons from queries	--gene-min-codons 300
Exclude genes shorter than 300 codons from contributing to function queries	--gene-min-codons 300 --function-sources
Exclude function queries with <300 codons	--function-min-codons 300
Exclude stop codons and single-codon amino acids	--exclude-amino-acids STP Met Trp
Exclude codons for amino acids with <5 codons in >90% of genes	--pansequence-min-amino-acids 5 0.9
Replace codons for amino acids with <5 codons in the gene or function with NaN	--sequence-min-amino-acids 5
Exclude queries with <300 codons involved in the CUB calculation	--query-min-analyzed-codons 300

Function codon count

Functions with fewer than a minimum number of codons can be ignored in the CUB analysis using --function-min-codons. Function codon count filters occur after gene codon count filters: the set of genes contributing to function codon frequency can be restricted by applying --gene-min-codons.

Analyzed query codon count

Filters removing codons from a gene or function query reduce the codon count factoring into the CUB calculation. --query-min-analyzed-codons ignores queries in the CUB calculation that have fewer than a minimum number of codons remaining. For example, --query-min-analyzed-codons 300 ensures that after removing codons by --exclude-amino-acids, --pansequence-min-amino-acids, and/or --sequence-min-amino-acids, queries must have 300 codons involved in the CUB calculation.

Edit this file to update this information.

Additional Resources

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.