title: PRIMED: PRIMEr database for deleting and tagging all fission and budding yeast genes developed using the open-source genome retrieval script (GRS).
abstract: The fission (Schizosaccharomyces pombe) and budding (Saccharomyces cerevisiae) yeasts have served as excellent models for many seminal discoveries in eukaryotic biology. In these organisms, genes are deleted or tagged easily by transforming cells with PCR-generated DNA inserts, flanked by short (50-100 bp) regions of gene homology. These PCR reactions use especially designed long primers, which, in addition to the priming sites, carry homology for gene targeting. Primer design follows a fixed method but is tedious and time-consuming especially when done for a large number of genes. To automate this process, we developed the Python-based Genome Retrieval Script (GRS), an easily customizable open-source script for genome analysis. Using GRS, we created PRIMED, the complete PRIMEr D atabase for deleting and C-terminal tagging genes in the main S. pombe and five of the most commonly used S. cerevisiae strains. Because of the importance of noncoding RNAs (ncRNAs) in many biological processes, we also included the deletion primer set for these features in each genome. PRIMED are accurate and comprehensive and are provided as downloadable Excel files, removing the need for future primer design, especially for large-scale functional analyses. Furthermore, the open-source GRS can be used broadly to retrieve genome information from custom or other annotated genomes, thus providing a suitable platform for building other genomic tools by the yeast or other research communities.
authors: Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, United States of America.
authors: Michael T
authors: MT
authors: Cummings
authors: Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, United States of America.
authors: Richard I
authors: RI
authors: Joh
authors: Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, United States of America.
authors: Mo
authors: M
authors: Motamedi
mesh_terms: D030541:Databases, Genetic; D017353:Gene Deletion; D005800:Genes, Fungal / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D016247:Information Storage and Retrieval; D058977:Molecular Sequence Annotation; D016133:Polymerase Chain Reaction; D004718:Saccharomycetales / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics*
references: Mol Cell. 2014 Jan 23;53(2):262-76
references: 24374313
references: G3 (Bethesda). 2014 Mar;4(3):389-98
references: 24374639
references: Nature. 2002 Feb 21;415(6874):871-80
references: 11859360
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Methods Enzymol. 1991;194:281-301
references: 2005793
references: Nucleic Acids Res. 1996 Sep 1;24(17):3469-71
references: 8811105
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5
references: 22110037
references: Yeast. 1998 Jul;14(10):943-51
references: 9717240
references: Yeast. 1998 Jul;14(10):953-61
references: 9717241
references: Yeast. 2006 Oct 15;23(13):921-8
references: 17072893
references: Methods Enzymol. 2010;470:759-95
references: 20946835
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9
references: 22039153
references: Nucleic Acids Res. 1997 Mar 1;25(5):1080-1
references: 9023122