Fast Plant Mitochondria Annotation

Using a set of known genes (43 core + 31 tRNA), we can predict how many of these occur in an angiosperm mitochondrial genome assembly. In this repository there is a set of HMM files (fastas/hmms) which describe these genes.

The executable here runs nhmmer on these genes across the mitochondrial genome of interest.

Requirements

You will need to direct the program to the executable path of nhmmer, and to a directory of HMMs (provided in this repository under ./hmms/).

fpma

The help page is as follows.

<Max Brown; Wellcome Sanger 2022>
Fast plant mito annotation (fmpa).
Version: 0.1.2

USAGE:
  fpma --plant-mito <PATH> --nhmmer-path <PATH> --hmms-path <PATH>
FLAGS:
  -h, --help            Prints help information
  -v, --version         Prints version information
ARGS:
  --plant-mito          Path to the plant mitochondrial genome
  --nhmmer-path         Path to the nhmmer executable (HMMER3)
  --hmms-path           Path to the directory containing a set of
                        HMM files. Download from:
                        https://github.com/tolkit/fpma/hmms/
OPTIONAL ARGS:
  --plot                Generate an HTML SVG of where the annotated
                        genes occur. Requires a name.
  --e-value             The E-value cut-off determining presence of
                        mito gene. <default 0.001>
  --gff                 Output a GFF3 file of gene locations.
                  
EXAMPLE:
  fpma --plant-mito ./mito.fasta --nhmmer-path ./nhmmer --hmms-path ./hmms/angiosperm_hmms/

Optionally an HTML plot is created. Please see the the docs for more detail on behind the scenes, and for a HTML plot preview.

Examples

Clone this repo to get the relevant code (fpma) & data (a bunch of HMMs).

# clone the repo
git clone https://github.com/tolkit/fpma
# install the binary to your path (REQUIRES RUST)
cd fpma && cargo install --path .

All ready to quickly annotate your plant mitochondrial genome. Say it's a flowering plant - the relevant HMM files are in the ./hmms/angiosperm_hmms directory.

# executed in the fpma cloned directory

# executable
fpma \
# path to your plant mito
--plant-mito path/to/your/mito.fasta \
# path to executable HMMER3
--nhmmer-path path/to/nhmmer \
# path to the angiosperm HMM directory
--hmms-path ./hmms/angiosperm_hmms/ \
# make an HTML plot with the name `mitome.html`
--plot mitome.html \
# make a GFF3 with name `mitome.gff`
--gff mitome.gff \
# add a very stringent E-value cut-off
--e-value 0.0000000000001 > out.txt
# out.txt contains a simple boolean matrix TSV
# of whether each gene was present in each fasta
# record in the input fasta

Disclaimer

This annotator is not supposed to be extremely complete nor accurate. The aim is just to determine the presence/absence of genes which should be present on a plant mitochondrion speedily and without hassle.