List of plastome annotation tools#
| year | Tool name | Publication | Type | Method | Organism | Comments |
|---|---|---|---|---|---|---|
| 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| 2007 | MFannot | Developed by the labs of B. Franz Lang and Gertraud Burger (unpublished) | pipeline | abinitio + similarity | annotation of mitochondrial and plastid genomes | output not easy to deal with.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! |
| 2015 | ORG.Annot | Developed by Eric Coissac (unpublished) | Pipeline | |||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 |
Interesting resource
https://chlorobox.mpimp-golm.mpg.de/Alternative-Tools.html