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Finding your way through Pneumocystis sequences in the NCBI gene database.
Christiane Weissenbacher-Lang1, Nora Nedorost, Herbert Weissenböck
1Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
The Journal of Eukaryotic Microbiology
|June 27, 2014
Summary
GenBank
Area of Science:
- Microbiology
- Bioinformatics
Background:
- Pneumocystis sequences are crucial for primer/probe design and phylogenetic studies.
- GenBank sequence data for Pneumocystis is often inconsistent due to nomenclature changes.
- This inconsistency hinders the practical use of available genetic information.
Purpose of the Study:
- To evaluate the completeness and information content of 532 Pneumocystis sequences from GenBank.
- To identify issues with nomenclature, genomic origin, host specification, and geographic data.
- To assess the usability of these sequences for research purposes.
Main Methods:
- Downloaded 532 Pneumocystis sequences from GenBank.
- Analyzed sequence metadata for completeness and accuracy.
- Evaluated parameters including nomenclature, genomic origin, host, and geographic information.
Main Results:
- Sequences were associated with multiple, often outdated, names.
- Nomenclature updates and "forma specialis" usage were inconsistently applied.
- Information on genomic origin, host, and geographic data was frequently incomplete or variable.
- Potential for downloading incorrect reference material was identified.
Conclusions:
- GenBank data for Pneumocystis requires significant improvement for reliable research use.
- Inconsistent metadata complicates primer design and phylogenetic analyses.
- A supplementary online database was created to provide detailed information for each accession number.
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