DOGMA pipeline

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 IN pipelines

 (14)
2018
PMCID: 5855747
PMID: 29425128
DOI: 10.3390/ijms19020525

[…] species to confirm the assembly with the uniformity of the iterative sequences., annotation of the transfer rnas (trnas), protein-coding genes, and ribosomal rnas (rrnas) was first performed using dogma v1.2 (university of texas at austin, austin, tx, usa) [59]. then, the protein-coding gene positions in the draft annotation were verified and if necessary manually adjusted following alignment […]

2018
PMCID: 5855824
PMID: 29463014
DOI: 10.3390/ijms19020602

[…] and assembled into complete chloroplast genomes by mapping to previously published whole chloroplast genome sequences. sequence gaps were resolved using sanger sequencing. genes were annotated using dogma [45] and blast. the newly constructed chloroplast genomes were deposited in the ddbj database under the accession numbers lc361349-51. finally, the circular chloroplast genome maps were drawn […]

2017
PMCID: 5460120
PMID: 28588246
DOI: 10.1038/s41598-017-03107-y

[…] pons et al.55. amplicons were sequenced using a junior ngs 454 platform and assembled into contigs in codoncode aligner (codoncode corporation, dedham, ma, usa). gene annotation was performed with dogma56 and mitos57 webservers., the aligned dataset comprised the nucleotide sequences of the 13 protein-coding mitochondrial genes (pcgs). nucleotide substitution saturation was assessed using […]

2016
PMCID: 4823975
PMID: 26957030
DOI: 10.1093/gbe/evv260

[…] 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). […]

2016
PMCID: 4856072
PMID: 26921295
DOI: 10.1534/g3.116.028175

[…] and p. gracilis, using the trinity transcriptome assembly tool with default parameters (haas et al. 2013). transcriptome sequences are already available for s. mediterranea (robb et al. 2008)., the dogma (wyman et al. 2004) and mitos (bernt et al. 2013) mt genome annotation tools were run on all genome assemblies to produce initial gene annotations. these annotations were additionally curated […]

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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