See here for the list of genome annotation tools
See here for the list of plastome annotation tools
See here for the list of plasmidome annotation tools
Back to the knowledge page
| year | Tool name | Publication | Type | Method | Organism | Comments | Output Format |
|---|---|---|---|---|---|---|---|
| 2004 | DOGMA | Wyman SK, Jansen RK and Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255 | animal mitochondrial and plant chloroplast | ||||
| 2007 | RNAweasel | Lang B.F., M-J. Laforest, and G. Burger (2007) Mitochondrial introns: a critical view. Trends Genet 23:119-25. | abinitio | based on RNA secondary structure profiles | mitochondrial RNAs only | ||
| 2007 | MFannot | Lang B.F., M-J. Laforest, and G. Burger (2007) Mitochondrial introns: a critical view. Trends Genet 23:119-25. | pipeline | abinitio + similarity | annotation of mitochondrial and plastid genomes | helpful with organelle genomes that contain lots of introns. Output not easy to deal with. AGAT can be used to convert the output in gff. | |
| 2010 | MITOFY | Alverson AJ, Wei X, Rice DW, Stern DB, Barry K and Palmer JD (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27: 1436-1448 | Plant mitochondrial | ||||
| 2010 | MOSAS | Sheffield NC, Hiatt KD, Valentine MC, Song H and Whiting MF (2010) Mitochondrial genomics in Orthoptera using MOSAS. Mitochondrial DNA 21: 87-104 | insect mitochondrial genome | ||||
| 2011 | MAKER2 | Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12, 491 (2011). | pipeline | Eukaryote, Prokaryote but alignment approach can be used for other type | It uses proteins, transcripts ... Abinitio: Augustus, Fgnesh,Genemark,snap. Need to modify the code to accept specific codon table for mitochondria. Not the best choice but provide nice protein alignments useful for manual curation | ||
| 2013 | MitoAnnotator | Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda, Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M and Nishida M (2013) MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution 30: 2531-2540 | Ab initio (sensors + Neural network) | Fish | MitoFish is a comprehensive and standardized fish mitochondrial genome database used by MitoAnnotator | ||
| 2013 | MITOS | Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M and Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69: 313-319 | metazoan mitochondrial genome | ||||
| 2014 | Prokka | Seemann T., Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063 | pipeline | Ab initio + evidence-based for functional annotation | prokaryote | https://github.com/tseemann/prokka Do structural and functional annotation. No intron allowed! | .gff, .gbk, .fna, .faa, .ffn, .sqn, .fsa, .tbl, .err, .log, .txt, .tsv |
| 2017 | Geseq | Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R and Greiner S (2017) GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11 | mitochondria and chloroplast | web based tool | |||
| 2018 | AGORA | Jung J, Kim JI, Jeong Y-S and Yi, G (2018) AGORA: organellar genome annotation from the amino acid and nucleotide references. Bioinformatics 34: 2661-2663 | organelle genome annotation ( mitochondrion and plastid genomes of eukaryotes ) | web application | |||
| 2019 | MitoZ | Yang C, Meng G, Liu S and Li Y (2019). MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, gkz173 | |||||
| year | Tool name | Publication | Type | Method | Organism | Comments | Output Format |
Interesting resource:
https://chlorobox.mpimp-golm.mpg.de/Alternative-Tools.html