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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
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1848)

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.

Key words

BLAST Enrichment Interactive map Bait design DNA sequence Protein sequence 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Katie Baker
    • 1
  • Gordon Stephen
    • 2
  • Shona Strachan
    • 3
    • 4
  • Miles Armstrong
    • 3
  • Ingo Hein
    • 3
    • 5
  1. 1.SynpromicsEdinburghUK
  2. 2.The James Hutton InstituteInformation and Computational SciencesDundeeUK
  3. 3.The James Hutton InstituteCell and Molecular SciencesDundeeUK
  4. 4.University of St Andrews, College GateSt AndrewsUK
  5. 5.Division of Plant Sciences at the James Hutton InstituteUniversity of Dundee, School of Life SciencesDundeeUK

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