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Protocols

DOGMA specifications

Information


Unique identifier OMICS_19238
Name DOGMA
Alternative name Dual Organellar GenoMe Annotator
Interface Web user interface
Restrictions to use None
Input data A file containing the complete nucleotide sequence of an animal mitochondrial or plant chloroplast genome.
Input format FASTA
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Stacia Wyman
  • person_outline Stacia Wyman

Publication for Dual Organellar GenoMe Annotator

DOGMA citations

 (358)
call_split

Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

2018
BMC Genomics
PMCID: 5946542
PMID: 29747572
DOI: 10.1186/s12864-018-4717-7
call_split See protocol

[…] tified using the software package tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) by eye, based on vertebrate mitochondrial anti-codon sequences and their secondary structure. In addition, the DOGMA annotation software was used to check annotated genes []. This procedure helped us to evaluate gene boundaries more carefully and to identify possible pseudo-genes []. The genome arrangements wi […]

call_split

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

2018
Sci Rep
PMCID: 5945635
PMID: 29749383
DOI: 10.1038/s41598-018-25759-0
call_split See protocol

[…] The 12 mitochondrial protein-coding genes and two ribosomal RNA genes of R. karukerae were identified using the annotation program DOGMA and ORF finder (NCBI), and were confirmed by comparing nucleotide sequences with those from closely related nematodes. Putative secondary structures of 22 tRNA genes were inferred using the prog […]

library_books

Re exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

2018
Sci Rep
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] cea (C), which were represented as AC-A and AC-C, respectively.The chloroplast genomes of the 28 genotypes were annotated for protein-coding genes, transfer RNA (tRNA), and ribosomal RNA (rRNA) using DOGMA (https://dogma.ccbb.utexas.edu/). The accuracy of the start and stop codons and intron–exon boundaries were manually annotated based on previously annotated information from the close relative A […]

library_books

The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution

2018
Front Plant Sci
PMCID: 5938401
PMID: 29765380
DOI: 10.3389/fpls.2018.00493

[…] For each species, the protein coding genes (PCGs), rRNAs, and tRNAs in the cp genome were predicted and annotated using Dual Organellar GenoMe Annotator (DOGMA) using the default parameters (). The positions of the start and stop codons, or intron/exon junctions of the PCGs, were manually corrected using a BLAST search […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] rors were propagated from erroneous references to newly assembled genomes creating a systematic problem in Solanaceae. For future reference we advise the jettison of outdated annotation tools such as DOGMA and advise the use of up-to-date novel software such as GeSeq to avoid complications. For de novo sequenced Solanaceae plastid genomes bittersweet can also serve as a novel reference for compari […]

library_books

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

2018
BMC Genomics
PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] clean reads were re-mapped to the draft genome and yielded the complete chloroplast genome sequences.Initial gene annotation of the three chloroplast genomes was performed through the online program Dual Organellar Genome Annotator []. Putative starts, stops, and intron positions were checked according to comparisons with homologous genes of H. parviflora cp genome using Geneious v9.0.5 software […]

Citations

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DOGMA institution(s)
Department of Computer Sciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA; Section of Integrative Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA

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