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.
Note: At this point the installation of MFannot is only possible on Unix systems (e.g. Ubuntu and CentOS).
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.
MFannot uses some well known programs, taht need to be installed on your system::
Further external programs and libraries that were developed in parallel to MFannot:
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:
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.
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.
In order to get the help page of MFannot you need to type mfannot -h in your terminal.
Please see CONTRIBUTING and CONDUCT for details.
GNU General Public License v3.0. Please see License File for more information.
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Digest
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475.6 MB
Last updated
almost 7 years ago
docker pull nbeck/mfannot_mini_ex2