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Species-Specific Genome Sequence Databases: A Practical Review
A D J van Dijk1,2,3
1Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. aaltjan.vandijk@wur.nl.
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.
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