Set of python scripts for mtDNA annotation. Run as:
python gff2gb.py fasta_file
Prerequisites:
-python (currently version 2.7 is supported)
-Biopython https://biopython.org/
(and several other python libraries easily installed with pip)
-wise2 https://www.ebi.ac.uk/~birney/wise2/, version 2.2 should be available for most linux distributions but recommended version is 2.4.1
-tmhmm https://services.healthtech.dtu.dk/software.php
-infernal http://eddylab.org/infernal/
-arwen http://130.235.244.92/ARWEN/arwen1.2.3.c
-glimmer3 http://ccb.jhu.edu/software/glimmer/index.shtml (needed icm profile for glimmer, included)
-critica http://www.life.illinois.edu/gary/programs/CRITICA/critica105b.tar.gz (need modified perl files for modern BLAST, included)
-vmatch http://www.vmatch.de/
-blast+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
-EMBOSS (getorf) ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz
-ViennaRNA package (with python bindings) https://github.com/ViennaRNA/ViennaRNA
-Databases:
+database of mitochondrial genomes, blast-formatted, with corresponding lineage specification (for mgcode and profile customization, included, can be customized at will)
+individual blast-formatted sub-databases of major clades (for critica, examples included)
+hmmer v2 profiles of mitochondrial proteins (included, these can be customized with hmmer)
+cm profiles of rRNAs and tRNAs (included, these can be customized with locarna, rRNA files must be indexed with cmpress from infernal package)
+pfam database (part A, hmm file pressed with hmmer, non-essential, not included)
Produces annotated GenBank file as well as several pdf and text files describing the features of the mitogenome (including tbl file needed for GenBank submission).
Several dependencies run on linux only but Win10 linux subsystem is also adequate. Everything is commandline-only.
Publication with some examples of usage is freely available at:
https://www.nature.com/articles/s41598-020-67976-6