title: Species-Specific Genome Sequence Databases: A Practical Review.
abstract: This chapter presents a use case illustrating the search for homologues of a known protein in species-specific genome sequence databases. The results from different species-specific resources are compared to each other and to results obtained from a more general genome sequence database (Phytozome). Various options and settings relevant when searching these databases are discussed. For example, it is shown how the choice of reference sequence set in a given database influences the results one obtains. The provided examples illustrate some problems and pitfalls related to interpreting results obtained from species-specific genome sequence databases.
authors.affiliation: Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. aaltjan.vandijk@wur.nl.|Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. aaltjan.vandijk@wur.nl.|Biometris, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. aaltjan.vandijk@wur.nl.
authors.forename: A D J
authors.initials: AD
authors.lastname: van Dijk
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D016678:Genome; D023281:Genomics / Q000379:methods; D057386:Search Engine; D013045:Species Specificity; D064878:Web Browser
keywords: BLAST; Genome sequence database