DOGMA

DOGMA is a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. The source code can be obtained at https://ebbgit.uni-muenster.de/domainWorld/DOGMA and a webserver to run your analysis directly in the browser without installation is available here.

DOGMA illustration (picture taken from [Kemena et al., NAR, 2019])

The figure shows schematically the method of DOGMA for example proteome data. The output of DOGMA gives you a completeness score measuring the quality of your proteome or transcriptome data from 0 - 100%.

On this website you can find additional data needed for evaluating your proteome/transcriptome. You will need the core sets (unless you want to create your own) and eventually our fast domain annotation tool RADIANT instead of PfamScan.

DOGMA is written in python and runs with any version from 2.7 on (including python 3). For help and instructions on how to use DOGMA please check the UserManual.

Core sets

To run DOGMA you need a core set with conserved protein domains you can compare your proteome/transcriptome data to. We provide several precomputed core sets for different clades that can be downloaded here for the newest DOGMA version:

core sets size (unzipped) pfam version comment
pfam32.tbz 91 MB (108 MB) pfam v32 Contains 11 core sets for pfam version 32 and has to be unpacked into the DOGMA folder.
pfam31.tbz 88 MB (104 MB) pfam v31 Contains 11 core sets for pfam version 31 and has to be unpacked into the DOGMA folder.

For core sets of older DOGMA and pfam versions please check here. Currently core sets for the following clades are included: eukaryotes, archaea, bacteria, arthropods, insects, vertebrates, mammals, fungi, plants, monocots and eudicots. Alternatively, you can create your own core sets. For more information about this or for information about the included species in the precomputed core sets please check the UserManual.

UProC not longer supported

With the release of our fast annotation tool RADIANT, which provides multiple advantages in combination with DOGMA compared to UProC, we canceled the UProC support.

The old databases for DOGMA version 2 can be still found here:

One of the options to annotate your data in DOGMA version 2 is via UProC. Unfortunately the developers of UProC do not provide databases for the newer Pfam versions. We therefore constructed them ourselves. They can be used without problems in connection with DOGMA. However, we do not recommend to use them for general annotation purposes as we are missing some domains.

Available UProC databases for different pfam versions can be found here.

Bugs and support (contact the developer)

If you find a problem, have questions or any kind of comment please contact us (domainworld[@]uni-muenster.de).

Citation

If you used DOGMA in your project please cite our publication:

Elias Dohmen, Lukas P.M. Kremer, Erich Bornberg-Bauer, and Carsten Kemena, DOGMA: domain-based transcriptome and proteome quality assessment, Bioinformatics (2016) 32 (17): 2577-2581. doi:10.1093/bioinformatics/btw231 http://bioinformatics.oxfordjournals.org/content/32/17/2577

Carsten Kemena, Elias Dohmen, Erich Bornberg-Bauer, DOGMA: a web server for proteome and transcriptome quality assessment, Nucleic Acids Research, gkz366, doi:10.1093/nar/gkz366 https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz366/5488015