PseudoHunter

Developed by Arkadiy Garber and John McCutcheon University of Montana, Biological Sciences Please send comments and inquiries to [email protected] ASCII art: https://manytools.org/hacker-tools/convert-images-to-ascii-art/

Pseudogene Identification Program

Reference-based identification of pseudogenes.

Inputs

To use this program, please provide contigs or gene-calls in FASTA format. If you would like to predict pseudogenes from previously-predicted gene calls, then you must supply a GFF file along with the gene-calls. Otherwise, PseudoHunter will take contigs in FASTA format and perform its own gene predictions using Prodigal.

Reference dataset

To use PseudoHunter must provide a reference dataset, which can consist of either contigs or gene-calls in FASTA format. This reference dataset can be a single genome, or a collection of genomes. PseudoHunter will use these genomes as a benchmark to predict which genes are pseudogenized in your dataset-of-interest; thus, you must be sure that whatever pseudogenization has occurred in your dataset is not also present in your reference genomes.

Intergenic regions

PseudoHunter can also identify pseudogenes in intergenic regions. In this case, please be sure to provide contigs in FASTA format (regardless of whether you are providing gene calls + GFF inputs). For example, you can provide gene-calls with an associated GFF file (with the -a, -n, and -gff argument), and also provide the raw contigs using the -q argument.

Output

Inside the output directory, you will find a CSV file names "summary.csv". This file will contain information on all predicted ORFs in your dataset, including which are predicted to be pseudogenes, as well as dN/dS ratios, proportion of exected gene length, fragmentation due to stop mutations, etc.

easy-installation with conda

git clone https://github.com/Arkadiy-Garber/PseudoHunter.git
cd PseudoHunter
./setup.sh
conda activate pseudo
PseudoHunter4.py -h

quickstart with raw contigs

PseudoHunter4.py -q contigs.fna -r referenceContigs.fna

quickstart with annotated genes

PseudoHunter4.py -n genesNucleicAcids.ffn -a genesAminoAcids.faa -rn referenceNucleicAcids.ffn -ra referenceAminoAcids.faa -gff genes.gff

quickstart with annotated genes and contigs

PseudoHunter4.py -n genesNucleicAcids.ffn -a genesAminoAcids.faa -rn referenceNucleicAcids.ffn -ra referenceAminoAcids.faa -gff genes.gff -q contigs.fna -out PseudoHunter_output

altering paramaters and skipping time-consuming steps by using previously-created output

PseudoHunter4.py -n genesNucleicAcids.ffn -a genesAminoAcids.faa -rn referenceNucleicAcids.ffn -ra referenceAminoAcids.faa -gff genes.gff -q contigs.fna -out PseudoHunter_output --skip -M 0.5