20. Growthpred

Growthpred

Predicting minimum generation time (MGT) and optimal growth temperature (OGT) for genomes/MAGs/SAGs

Please cite the original paper if you use this tool:
Vieira-Silva S, Rocha EPC (2010) The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics. PLOS Genetics 6(1): e1000808. https://doi.org/10.1371/journal.pgen.1000808

Requires ncbi-blast and R modules loaded.

Important:

in ./Programs/get_rprots.sh change shebang line to !#bin/bash

in ./Programs/get_rprots.sh change

$4 -p blastx -d $2 -i $3.plen.tmp -m 8 -e 0.00001 > $3.blast.all

to if you don't have legacy blast available

blastx -db $2 -query $3.plen.tmp -outfmt 6 -evalue 0.00001 > $3.blast.all

Usage:

python growthpred-v1.07.py -S -c 0 -o input_results -b -t -r -g input.genes.fna

Options:

GROWTHPRED VERSION 1.07
Usage: growthpred-v1.07.py [options]

Options:
  -h, --help            show this help message and exit
  -f HEG, --heg=HEG     File of highly expressed genes (DNA, FASTA)
  -g OTH, --nonheg=OTH  Complete genome (DNA, FASTA)
  -o OUTFILE            Name of output file
  -c CODE               0 : Universal; 1 : Yeast mitochondrial; 2 : Vertebrate
                        mitochondrial; 3 :
                        Mold/Protozoan/Mycoplasma/Spiroplasma; 4 :
                        Invertebrate mitochondrial; 5 : Candida cylindracea; 6
                        : Ciliate; 7 : Euplotes; 8 : Echinoderm mitochondrial
  -s                    Ignore first (start) codons
  -S                    Ignore last  (stop)  codons
  -T OGT                Optimal growth temperature (Celsius)
  -t                    Estimate optimal growth temperature
  -b                    Retrieve ribosomal protein genes by blast
  -r                    Recover file with ribosomal protein genes retrieved by
                        blast
  -i                    Recover file with codon usage bias indexes for each
                        gene
  -m                    Metagenome or mixed organisms sequences
  -e                    Use E. coli K12 example files