PMID- 30182237
OWN - NLM
STAT- MEDLINE
DCOM- 20190501
LR  - 20190501
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 1848
DP  - 2018
TI  - 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.
PG  - 199-206
LID - 10.1007/978-1-4939-8724-5_14 [doi]
AB  - 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.
FAU - Baker, Katie
AU  - Baker K
AD  - Synpromics, Edinburgh, UK.
FAU - Stephen, Gordon
AU  - Stephen G
AD  - The James Hutton Institute, Information and Computational Sciences, Dundee, UK.
FAU - Strachan, Shona
AU  - Strachan S
AD  - The James Hutton Institute, Cell and Molecular Sciences, Dundee, UK.
AD  - University of St Andrews, College Gate, St Andrews, UK.
FAU - Armstrong, Miles
AU  - Armstrong M
AD  - The James Hutton Institute, Cell and Molecular Sciences, Dundee, UK.
FAU - Hein, Ingo
AU  - Hein I
AD  - The James Hutton Institute, Cell and Molecular Sciences, Dundee, UK. 
      Ingo.Hein@hutton.ac.uk.
AD  - Division of Plant Sciences at the James Hutton Institute, University of Dundee, 
      School of Life Sciences, Dundee, UK. Ingo.Hein@hutton.ac.uk.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
SB  - IM
MH  - Computational Biology/*methods
MH  - Databases, Genetic
MH  - Host-Pathogen Interactions/*genetics/immunology
MH  - Sequence Analysis, DNA
MH  - *Software
MH  - User-Computer Interface
OTO - NOTNLM
OT  - BLAST
OT  - Bait design
OT  - DNA sequence
OT  - Enrichment
OT  - Interactive map
OT  - Protein sequence
EDAT- 2018/09/06 06:00
MHDA- 2019/05/02 06:00
CRDT- 2018/09/06 06:00
PHST- 2018/09/06 06:00 [entrez]
PHST- 2018/09/06 06:00 [pubmed]
PHST- 2019/05/02 06:00 [medline]
AID - 10.1007/978-1-4939-8724-5_14 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2018;1848:199-206. doi: 10.1007/978-1-4939-8724-5_14.