Species-specific genome sequence databases: A practical review

Aalt-Jan van Dijk*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish
Title of host publicationPlant genomics databases
Subtitle of host publicationMethods and Protocols
EditorsAalt D.J. van Dijk
PublisherHumana Press Inc.
ISBN (Electronic)9781493966585
ISBN (Print)9781493966561
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745



  • Genome sequence database

Cite this

van Dijk, A-J. (2017). Species-specific genome sequence databases: A practical review. In A. D. J. van Dijk (Ed.), Plant genomics databases: Methods and Protocols (pp. 173-181). (Methods in Molecular Biology; Vol. 1533). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6658-5_9