Automatic annotation of organellar genomes with DOGMA

By Stacia K. Wyman, Robert K. Jansen, Jeffrey L. Boore. Bioinform., 2004

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View Paper: https://www.semanticscholar.org/paper/f1370b6409b05dbb22ab44586a9bf2dae052c621

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In Molecular Biology

Citations in the corpus

Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes (2019, methodology): “The first published computational method to annotate mitogenomes was DOGMA (14).”
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, methodology): “Thus, separate software, likeDOGMA (29),MOSAS (30),MITOS (31) are required for the following genome annotation (32).”
MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline (2013, methodology): “DOGMA (Wyman et al. 2004) is a pioneering tool in this field that helps researchers annotate mitochondrial and chloroplast genomes in a semiautomatic manner.”
Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids (2015, methodology): “Gene annotation of plastomes was performed in DOGMA (Wyman et al., 2004).”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, background): “However, to our knowledge, there is only one web server, DOGMA, which is able to annotate chloroplast genomes specifically [20].”
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1 (2010, methodology): “Genes were annotated and gene sequences were extracted from assemblies using the DOGMA webserver (,http:// dogma.ccbb.utexas.edu., Wyman et al., 2004, and see below).”
IRscope: an online program to visualize the junction sites of chloroplast genomes (2018, methodology): “Files can be also uploaded manually in a DOGMA output format (Wyman et al., 2004) accompanied with a fasta file and/or the coordinates of the IR junctions.”
GeSeq – versatile and accurate annotation of organelle genomes (2017, background): “DOGMA (5) annotates chloroplast and animal mitochondrial sequences, but no plant mitochondrial genomes.”
OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes (2019, background): “, GetOrganelle or IOGA; (4,5)], and we are currently aware of no less than twelve (semi-)automatic annotation tools for organellar genomes (1,3,6-15).”
Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales (2009, methodology): “Wyman SK, RK Jansen, JL Boore 2004 Automatic annotation of organellar genomes with DOGMA.”
How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research (2014, background): “DOGMA (Wyman et al., 2004) was the first package developed; however, its internal database of curated mt genomes is now extremely out of date – no new mt genomes have been added since mid-2004 and just 25 insect species are included.”
CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “In the past few years, several annotations and visualization tools have been developed for organelle genomes; these tools include DOGMA (Wyman et al., 2004), CPGAVAS (Liu et al., 2012), Plann (Huang & Cronk, 2015), Verdant (McKain et al., 2017), GeSeq (Tillich et al., 2017 ), AGORA (Jung et al.,…”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “Numerous other tRNA detection and classification methods have become available since tRNAscan-SE was first developed, including ARAGORN (6), which detects both tRNA genes and tmRNA genes; DOGMA (7), ARWEN (8), and MiTFi (9), which are designed for annotating tRNA genes in various types of organellar”