DOGMA: a Web Server for Proteome and Transcriptome Quality Assessment

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 May 12

PMID 31076763

Citations 8

Authors

Carsten Kemena

Elias Dohmen

Erich Bornberg-Bauer

Affiliations

Soon will be listed here.

Abstract

Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment represents a crucial step prior to downstream analyses on novel transcriptomes and proteomes. DOGMA allows such a quality assessment to be carried out. The data of interest are evaluated based on a comparison with a core set of conserved protein domains and domain arrangements. Depending on the studied species, DOGMA offers precomputed core sets for different phylogenetic clades. We now developed a web server for the DOGMA software, offering a user-friendly, simple to use interface. Additionally, the server provides a graphical representation of the analysis results and their placement in comparison to publicly available data. The server is freely available under https://domainworld-services.uni-muenster.de/dogma/. Additionally, for large scale analyses the software can be downloaded free of charge from https://domainworld.uni-muenster.de.

Citing Articles

Transcriptomics, Proteomics and Bioinformatics in Atrial Fibrillation: A Descriptive Review.

Belfiori M, Lazzari L, Hezzell M, Angelini G, Dong T Bioengineering (Basel). 2025; 12(2).

PMID: 40001669 PMC: 11851880. DOI: 10.3390/bioengineering12020149.

Comparative Evolutionary Genomics in Insects.

Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans A Methods Mol Biol. 2024; 2802:473-514.

PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16.

Quality assessment of gene repertoire annotations with OMArk.

Nevers Y, Warwick Vesztrocy A, Rossier V, Train C, Altenhoff A, Dessimoz C Nat Biotechnol. 2024; 43(1):124-133.

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A high-quality genome assembly of the waterlily aphid Rhopalosiphum nymphaeae.

Wang Y, Xu S Sci Data. 2024; 11(1):194.

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Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes.

Feron R, Waterhouse R Gigascience. 2022; 11.

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