Species-specific genome sequence databases: A practical review

Aalt-Jan van Dijk*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-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.

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

Keywords

  • BLAST
  • Genome sequence database

Fingerprint Dive into the research topics of 'Species-specific genome sequence databases: A practical review'. Together they form a unique fingerprint.

Cite this