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Finding your Way Through Pneumocystis Sequences in the NCBI Gene Database
Author(s) -
WeissenbacherLang Christiane,
Nedorost Nora,
Weissenböck Herbert
Publication year - 2014
Publication title -
journal of eukaryotic microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.067
H-Index - 77
eISSN - 1550-7408
pISSN - 1066-5234
DOI - 10.1111/jeu.12132
Subject(s) - genbank , uniprot , accession number (library science) , phylogenetic tree , biology , nomenclature , identifier , sequence database , species name , database , genetics , computational biology , information retrieval , computer science , gene , programming language , taxonomy (biology) , botany
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.

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