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AAI Calculation
comparem is a toolbox for comparative genomics. We are using it to calculate AAI (Average Amino Acid Identity) between genomes. It is installed into a conda env within SCGC's anaconda3 module, so to access it you need to enter:
module use /mod/scgc
module load anaconda3
source activate comparem
To see what comparem can do, type:
$ comparem -h
Output:
...::: CompareM v0.0.23 :::...
Common workflows:
aai_wf -> Calculate AAI between all pairs of genomes
(runs call_genes => similarity => aai)
classify_wf -> Identify similar genomes based on AAI values
(runs call_genes => similarity => classify)
Gene prediction:
call_genes -> Identify genes within genomes
Gene homology and genome similarity:
similarity -> Perform reciprocal sequence similarity search between proteins
aai -> Calculate AAI between all pairs of genomes
classify -> Identify similar genomes based on AAI value
Usage profiles:
aa_usage -> Calculate amino acid usage within each genome
codon_usage -> Calculate codon usage within each genome
kmer_usage -> Calculate kmer usage within each genome
stop_usage -> Calculate stop codon usage within each genome
Lateral gene transfer:
lgt_di -> Calculate dinuceotide (3rd,1st) usage of genes to identify putative LGT events
lgt_codon -> Calculate codon usage of genes to identify putative LGT events
Visualization and exploration:
diss -> Calculate the dissimilarity between usage profiles
hclust -> Perform hierarchical clustering
Use: comparem <command> -h for command specific help.
Feature requests or bug reports can be sent to Donovan Parks ([email protected])
or posted on GitHub (https://github.com/dparks1134/comparem).
For instructions on CompareM's aai calculation workflow type:
$ comparem aai_wf -h
Output:
usage: comparem aai_wf [-h] [-e EVALUE] [-p PER_IDENTITY] [-a PER_ALN_LEN]
[-x FILE_EXT] [--proteins] [--force_table FORCE_TABLE]
[--blastp] [--sensitive] [--keep_headers] [--keep_rbhs]
[--tmp_dir TMP_DIR] [-c CPUS] [--silent]
input_files output_dir
Calculate AAI between all pairs of genomes
positional arguments:
input_files genome files
output_dir output directory
optional arguments:
-h, --help show this help message and exit
-e, --evalue EVALUE e-value cutoff for identifying initial blast hits
(default: 0.001)
-p, --per_identity PER_IDENTITY
percent identity for defining homology (default: 30.0)
-a, --per_aln_len PER_ALN_LEN
percent alignment length of query sequence for
defining homology (default: 70.0)
-x, --file_ext FILE_EXT
extension of files to process (default: fna)
--proteins indicates the input files contain protein sequences
--force_table FORCE_TABLE
force use of specific translation table
--blastp use blastp instead of diamond
--sensitive use sensitive mode of DIAMOND
--keep_headers indicates FASTA headers already have the format
<genome_id>~<gene_id>
--keep_rbhs create file with reciprocal best hits
--tmp_dir TMP_DIR specify alternative directory for temporary files
(default: /tmp)
-c, --cpus CPUS number of CPUs to use (default: 1)
--silent suppress output
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