BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing

Katie Baker, Gordon Stephen, Shona Strachan, Miles Armstrong, Ingo Hein (Lead / Corresponding author)

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Numerous genes that determine the outcome of plant-pathogen interactions are currently being discovered and include, for example, immune receptors, susceptibility factors and pathogen effectors and their host targets. Target enrichment sequencing provides a means to preferentially resequence these genes of interest without the need to first generate a genotype-specific genome assembly. The Basic Local Alignment Search Tool (BLAST), in combination with the here developed BLASTmap, can be used to design probes that specifically target such gene(s), either by using the target species or the closest related genus as a reference. BLAST is a ubiquitous tool in biological sequence analysis and a multitude of programs are available for the visualization of BLAST alignments. However, there are currently no dedicated programs for visual comparison of large-scale BLAST output attributes such as bit score. The need to quickly and efficiently compare many thousands of BLAST results led to the development of BLASTmap, an interactive web application created using the Shiny R package, customized for clustering and viewing BLAST results as an interactive heat map. Here we show an example of how BLASTmap was successfully applied to analyze custom DNA/RNA probe sequences and to visually determine that four probes are sufficient for the specific yet inclusive enrichment of the potato R2 disease resistance gene family.

Original languageEnglish
Title of host publicationPlant Pathogenic Fungi and Oomycetes
EditorsWenbo Ma, Thomas Wolpert
Place of PublicationNew York
PublisherHumana Press
Pages199-206
Number of pages8
Volume1848
ISBN (Electronic)9781493987245
ISBN (Print)9781493987238
DOIs
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
PublisherSpringer Verlag
ISSN (Print)1064-3745

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Keywords

  • BLAST
  • Bait design
  • DNA sequence
  • Enrichment
  • Interactive map
  • Protein sequence

Cite this

Baker, K., Stephen, G., Strachan, S., Armstrong, M., & Hein, I. (2018). BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing. In W. Ma, & T. Wolpert (Eds.), Plant Pathogenic Fungi and Oomycetes (Vol. 1848, pp. 199-206). (Methods in Molecular Biology). Humana Press. https://doi.org/10.1007/978-1-4939-8724-5_14