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


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 


  1. 1.
    Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, McCombie WR (2011) A comparative analysis of exome capture. Genome Biol 12:R97CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Lighten J, van Oosterhout C, Paterson IG, Mcmullan M, Bentzen P (2014) Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata). Mol Ecol Resour 14:753–767CrossRefPubMedGoogle Scholar
  3. 3.
    Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, Etherington GJ et al (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J 76:530–544CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Giolai M, Paajanen P, Verweij W, Percival-Alwyn L, Baker D, Witek K et al (2016) Targeted capture and sequencing of gene sized DNA molecules. BioTechniques 61:315–322CrossRefPubMedGoogle Scholar
  5. 5.
    Witek K, Jupe F, Witek AI, Baker D, Clark MD, Jones JDG (2016) Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing. Nat Biotechnol 34:656–660CrossRefPubMedGoogle Scholar
  6. 6.
    Van Weymers PSM, Baker K, Chen X, Harrower B, Cooke DEL, Gilroy EM et al (2016) Utilizing “Omic” technologies to identify and prioritize novel sources of resistance to the oomycete pathogen Phytophthora infestans in potato germplasm collections. Front Plant Sci 7:672PubMedPubMedCentralGoogle Scholar
  7. 7.
    Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A et al (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111–118CrossRefPubMedGoogle Scholar
  8. 8.
    Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridisation probes from plasmids containing a bacteriophage SP6 promotor. Nucl Acids Res 12:7035–7056CrossRefPubMedGoogle Scholar
  9. 9.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  10. 10.
    Neumann RS, Kumar S, Shalchian-Tabrizi K (2014) BLAST output visualization in the new sequencing era. Brief Bioinform 15:484–503CrossRefPubMedGoogle Scholar
  11. 11.
    Gehlenborg N, Wong B (2012) Points of view: into the third dimension. Nat Methods 9:851–851CrossRefPubMedGoogle Scholar
  12. 12.
    Khomtchouk BB, Van Booven DJ, Wahlestedt C (2014) HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. Source Code Biol Med 9:30CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Yachdav G, Hecht M, Pasmanik-Chor M, Yeheskel A, Rost B (2014) HeatMapViewer: interactive display of 2D data in biology. F1000Research 48:1–6Google Scholar
  14. 14.
    Metsalu T, Vilo J (2015) ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res 43:566–570CrossRefGoogle Scholar
  15. 15.
    R Core Team (2015) R: A language and environment for statistical computing. Available from:
  16. 16.
    R Studio Team (2015) RStudio: Integrated Development for R. Available from:
  17. 17.
    Destefanis M, Nagy I, Rigney B, Bryan GJ, McLean K, Hein I et al (2015) A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages. BMC Plant Biol 15:255CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421CrossRefPubMedPubMedCentralGoogle Scholar

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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