DOGMA specifications

Information


Unique identifier OMICS_19238
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 <>

DOGMA article

DOGMA citations

 (6)
2017
PMCID: 5737380

[…] cost = 3, deletion cost = 3, length fraction = 0.5, and similarity fraction = 0.8. plastome maps were visualized by using circos 0.67 (krzywinski etal. 2009)., gene prediction was performed in dogma (wyman etal. 2004) and trna genes were predicted by using trnascan-se 1.21 (schattner etal. 2005). the boundaries of predicted genes/exons were confirmed by aligning them with their orthologous […]

2016
PMCID: 4823975

[…] genomes, and any gaps that were present were resolved by mapping the raw reads to the assembly., the three complete plastid genomes were annotated using the plastid genome annotation package dogma (wyman et al. 2004). intron positions, as well as start and stop codons of protein-coding genes, were manually adjusted, if necessary, based on the four reference genomes (see above). […]

2015
PMCID: 4655330

[…] the university of maryland’s genomic resource center. the annotated plastome sequence has been deposited in genbank (kt428297) and the illumina reads are in sra305491., primary annotations involved dogma63, confirmation with the glycine max reference (nc_007942), open reading frame confirmation for protein coding genes using geneious, and trna boundary confirmation/correction using the trnascan […]

2014
PMCID: 4044308

[…] 500 bp, and the largest contig was 13,610 bp. gaps were filled by pcr. all sequenced contigs were de novo assembled using geneious 6.1.2 (kearse et al., 2012). gene annotations were performed by dogma (wyman et al., 2004) and trnascan (lowe and eddy, 1997). then, the exact positions of all genes were determined by local blast searches using the gene database of ferns obtained from ncbi., […]

2013
PMCID: 3696114

[…] followed with manual corrections for start codons. intron positions were determined based on those of p. dactylifera [21] and elaeis guineensis [22]. the transfer rna genes were annotated using dogma and trnascan-se (version1.23) [23]. some intron-containing genes in which exons are too short to be detected were identified based on comparisons to corresponding exons in p. dactylifera and e. […]

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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