See here for the list of genome annotation tools
See here for the list of mitome 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 | plant chloroplast and animal mitochondrial | ||||
| 2007 | MFannot | Developed by the labs of B. Franz Lang and Gertraud Burger (unpublished) | pipeline | abinitio + similarity | annotation of mitochondrial and plastid genomes | output not easy to deal with. AGAT can be used to convert the output in gff | |
| 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 | ||
| 2012 | CpGAVAS | Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X and Guan X (2012) CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13: 715 | web based tool | ||||
| 2013 | CGAP | Cheng J, Zeng Xu, Ren G and Liu Z (2013) CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes. BMC Bioinformatics 14:95 | comparative | ||||
| 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 | Do structural and functional annotation. No intron allowed! | .gff, .gbk, .fna, .faa, .ffn, .sqn, .fsa, .tbl, .err, .log, .txt, .tsv |
| 2015 | ORG.Annot | Developed by Eric Coissac (unpublished) | Pipeline | ||||
| 2015 | Plann | Plann: A command‐line application for annotating plastome sequences. DI Huang, QCB Cronk. Applications in Plant Sciences 3 (8), 1500026, 2015. 226, 2015. | chloroplast genome annotation | ||||
| 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 | chloroplast mitochondria | web based tool | |||
| 2017 | Verdant | McKain MR, Hartsock RH, Wohl MM, Kellogg EA. 2017. Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. Bioinformatics. 33:130–132. | chloroplast | ||||
| 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 | CpGAVAS2 | Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L and Liu C (2019) CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research, gkz345 | |||||
| year | Tool name | Publication | Type | Method | Organism | Comments | Output Format |
Interesting resource:
https://chlorobox.mpimp-golm.mpg.de/Alternative-Tools.html