DOGMA - Help page

DOGMA (DOmain-based General Measure for transcriptome and proteome quality Assessment) is a program to estimate the quality of a given set of sequences. A typical use case is to assess the quality of a newly assembled transcriptome or the newly annotated proteome of a genome. On this page you will find information concerning the usage of the DOGMA web server.


The algorithm

The principle of the DOGMA algorithm is simple: A known set of conserved domain arrangements (CDAs) are compared with the annotated domain arrangements of a proteome/transcriptome to analyse. DOGMA returns the percentage of found CDAs, indicating the quality of the analysed proteome/trancriptome.
Overview of the DOGMA quality assessment algorithm
For more information on how the algorithm works, please have a look at the publication of DOGMA

The web service

This chapter describes the web server functions

Starting DOGMA


DOGMA provides a simple interface to determine the data to analyse:
The DOGMA input section
The easiest and fastest is to directly upload your annotation file. The highest accuracy and most detailed results can be expected when using Pfam annotations of your isoform free proteome. In case the proteome has isoforms it is recommended to create a new file containing only the longest ones. We additionally accept RADIANT annotations as well, but please be aware of the current limitations when using RADIANT (see RADIANT for more information).

If you provide a sequence file in FASTA format containing proteins or spliced genes instead, the server will run RADIANT first to annotate the sequences with domains. RADIANT is a very fast domain annotation program that in general works very well together with DOGMA. However, when annotating species whose domains are very distinct from the ones in the Pfam database, RADIANT might perform poorly and therefore lower the DOGMA score (see RADIANT for more information). It is not possible to analyse whole genomes/assemblies as only a single ORF per sequence will be predicted.

You have as well the option to use one of the provided example files for a test run. After having selected an example file, the "Show example" button can be used to open the file in a text editor of your choice. If you press "Run" DOGMA will be executed with the selected example file. You can simply use the default parameters for these files.

If you provide nucleotide sequences you have to check the translate button. It will translate the sequences into amino acids by predicting the longest ORF in all 6 frames.


This section will explain the different parameters that you can choose to influence the behaviour of DOGMA.
DOGMA parameters
The DOGMA parameter section
DOGMA mode
The DOGMA mode influences how the DOGMA score is calculated. The proteome mode provides better accuracy estimations because it can take into account the number of found CDAs for each CDA type. Therefore, an isoform free sequence set is needed for a correct calculation. As there is no general way to identify them you will have to provide one. The transcriptome mode on the other hand completely ignores the exact number of specific CDAs and only checks for presence or absence.
Pfam version
If you provide the domain annotation directly, you should choose here the same Pfam version you used to annotate your sequences. If you provide sequences, this choice will determine which Pfam version will be used to annotate them.
Choice of core set
The core set defines the set of domains that is compared to the sequences to be analysed. We provide precomputed core sets for different clades. For best results choose the most specific core set available as it will contain a higher number of domains to which can be compared and therefore provides a higher accuracy.

Result interpretation

The result page of DOGMA will display the DOGMA analysis results. Additionally, the used parameters are shown.

DOGMA score

The main result of DOGMA is summarized in a table. It compares the number of found conserved domain arrangements (CDAs) with the expected number from the core set. Separate values for CDAs of length 1,2 and 3 are provided. Furthermore, the last row shows the total percentage, the DOGMA score.

CDAsize #Found #Expected %Completeness
1 1036 1051 98.57
2 428 441 97.05
3 161 167 96.41
Total 1625 1659 97.95

Additionally, a graphic relates your DOGMA score to a larger set of known proteomes. The graphic compares the quality of your proteome/transciptome (red dot) to a precomputed set of DOGMA scores which belong to the same clade as the chosen core set. With the exception of archaea, the proteomes for the comparisons were all taken from ensembl databases. The proteomes for the archaea comparison are from different sources.
DOGMA example comparison
An example of the comparison result. The red dot shows how your data compares to a set of known proteomes of the same core set. The vertical blue line denotes the median. The width of the blue area denote the density of proteomes with this DOGMA score.

Partial domain analysis

This analysis is only available when a PFAM annotation was provided. The partial domain analysis calculates the general occurrence of partial domains in your proteome set and is not limited to the domains in the core set. A domain is considered to be partial if its length is shorter than half of the expected size. An example can be seen below:

fraction of partial domains: 3.99%
number of partial domains: 1750
total number of domains: 43871
coverage threshold: 0.5

Missing CDAs

This section displays a detailed overview of the missing CDAs of your data. They are sorted by size. If you hover over a domain it will show you the name of the Domain. The domain itself is a link to the Pfam entry of it.
DOGMA missing example
Listing of missing CDAs of size 3.


RADIANT is a program we are currently developing. It allows to annotate a proteome in a few minutes with domains. The very fast annotation allows its usage on a web server. However, while in the majority of the cases the domain annotation is actually very good and has very little influence on the DOGMA score, in some cases it does perform poorly which influences (decreases) the DOGMA score although the proteome/transcriptome is of good quality. We therefore recommend RADIANT to be used only to get a first fast impression of the quality and perform afterwards a check with a Pfam annotation (especially in cases when the DOGMA score is low).

How to cite

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

Browser compatibility

We have tested this website on a wide range of operating systems and browsers:
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Linux Ubuntu 18.04 63.0.3 not tested n/a n/a 57.0.3098.76
Windows 10 60.3.0esr 70.0.3538.110 41.16299.655.0 n/a not tested
MacOS Mojave 10.14.1 63.0.3 70.0.3538.110 n/a 12.0.1 57.0.3098.76
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