MFannot

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

MFannot is particularly helpful with organelle genomes that contain lots of introns. Intron-exon boundaries are identified by a combination of secondary structure, intron splice rules and exon similarities, and are thus precise in most instances. Note that not all introns may be detected by MFannot, which requires expert manual curation/completion of gene structure annotations before GenBank submission.

The output of MFannot is a listings of gene coordinates either in Sequin format, a format that can be directly loaded into NCBI's sequence submission tools, or in Masterfile format (computer-parsible as well as human-readable; annotations embedded into the FASTA sequence).

This package is based on activities of the OGMP (Organelle Genome Megasequencing Project, Département de Biochimie, Université de Montréal, circa 1990-1998) and further developed since then by the labs of B.F. Lang and G. Burger.

Installation

Note: At this point the installation of MFannot is only possible on Unix systems (e.g. Ubuntu and CentOS).

BioPerl

MFannot is a PERL pipeline that use BioPerl, so you need to install BioPerl first and at least install the Bio::AlignIO and all their dependencies.

External programs

MFannot uses some well known programs, taht need to be installed on your system::

Blast (requires version 2.2.26 and version >= 2.2.27+): to install Blast see the documentation at the NCBI website.
- tested on version 2.2.26 and 2.2.31+
HMMER: to install HMMER see the documentation at the HMMER website.
- tested on version 3.2.1
Exonerate: to install Exonerate see the documentation at the following GitHub repo.
- tested on version 2.2.0
Muscle: to install Muscle see the documentation here.
- tested on version muscle-3.8.1551
EMBOSS: to install EMBOSS see the documentation here.
- tested on version 6.6.0
Erpin: to install Erpin see the documentation here.
- tested on version 5.5.4.serv
tbl2asn: to install tbl2asn see the documentation here
PirObject: to install this Perl library see the documentation in this GitHub repo,

Internal programs

Further external programs and libraries that were developed in parallel to MFannot:

PirModels: all the PirModels needed by umac, HMMsearchWC and other programs developped at OGMP, to install the PirModels see the documentation in this GitHub repo.
Flip:to install Flip see the documentation in this GitHub repo
Umac: to install Umac see the documentation in this GitHub repo
HMMSearchWC: to install HMMSearchWC see the documentation in this GitHub repo
RNAfinder: to install RNAfinder see the documentation in this GitHub repo
Mf2sqn: to install Mf2sqn see the documentation in this GitHub repo
grab-seq and grab-fasta: to install this two tools see the documentation in this GitHub repo
MFannot: to install MFannot see the documentation in this GitHub repo

Static Data

MFannot needs some static data files to run; these contain data defining splice sites, reference protein sequences, HMM models, etc. These files are all available as a single bundle in this GitHub repo.

In order to run MFannot you should setup the following environment variable:

EGC to point to MFannot_data/EGC.
MFANNOT_EXT_CFG_PATH to point to MFannot_data/config.
MFANNOT_MOD_PATH to point to MFannot_data/models.
ERPIN_MOD_PATH to point to MFannot_data/models/Erpin_models.
MFANNOT_LIB_PATH to point to MFannot_data/protein_collections.

BLAST matrices

Download BLAST matrices from the ncbi ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/* (eg: wget -r -np -nd -P /path/to/mfannot/blast_matrices ftp://ftp.ncbi.nlm.nih.gov/blast/matrices) and set the environment variable BLASTMAT to point to the directory where you have download the matrices.

Docker container

The entire software package, including data files, is available in a Docker container. You can find this docker container on DockerHub and use it in order to run MFannot locally if you do not want to install everything.

The process to install MFannot on Ubuntu14 within a Docker image is documented in the [Dockerfile] present in this repository.

Usage

In order to get the help page of MFannot you need to type mfannot -h in your terminal.

Contributing

Please see CONTRIBUTING and CONDUCT for details.

Credits

All Contributors

License

GNU General Public License v3.0. Please see License File for more information.

License

BFL-lab/Mfannot

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