title: Finding your way through Pneumocystis sequences in the NCBI gene database.
abstract: Pneumocystis sequences can be downloaded from GenBank for purposes as primer/probe design or phylogenetic studies. Due to changes in nomenclature and assignment, available sequences are presented with a variety of inhomogeneous information, which renders practical utilization difficult. The aim of this study was the descriptive evaluation of different parameters of 532 Pneumocystis sequences of mitochondrial and ribosomal origin downloaded from GenBank with regard to completeness and information content. Pneumocystis sequences were characterized by up to four different names. Official changes in nomenclature have only been partly implemented and the usage of the "forma specialis", a special feature of Pneumocystis, has only been established fragmentary in the database. Hints for a mitochondrial or ribosomal genomic origin could be found, but can easily be overlooked, which renders the download of wrong reference material possible. The specification of the host was either not available or variable regarding the used language and the localization of this information in the title or several subtitles, which limits their applicability in phylogenetic studies. Declaration of products and geographic origin was incomplete. The print version of this manuscript is completed by an online database which contains detailed information to every accession number included in the meta-analysis.
authors: Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
authors: Christiane
authors: C
authors: Weissenbacher-Lang
authors: Nora
authors: N
authors: Nedorost
authors: Herbert
authors: H
authors: Weissenböck
mesh_terms: D001483:Base Sequence; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D030561:Databases, Nucleic Acid; D008969:Molecular Sequence Data; D011010:Pneumocystis / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal
keywords: GenBank; geographic origin; host specification; information content; meta-analysis; mitochondrial and ribosomal genomic origin; nomenclature; online database