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

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.

Original languageEnglish
Title of host publicationPlant genomics databases
Subtitle of host publicationMethods and Protocols
EditorsAalt D.J. van Dijk
PublisherHumana Press Inc.
Pages173-181
ISBN (Electronic)9781493966585
ISBN (Print)9781493966561
DOIs
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1533
ISSN (Print)1064-3745

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Keywords

  • BLAST
  • 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