This is an example data set for BLAST data generated with standalone BLAST from NCBI.
data(RFLPdata)
A data frame with 737 observations on the following four variables
query.id
character: sequence identifier.
subject.id
character: subject identifier.
identity
numeric: identity between sequences (in percent).
alignment.length
integer: number of nucleotides.
mismatches
integer: number of mismatches.
gap.opens
integer: number of gaps.
q.start
integer: query sequence start.
q.end
integer: query sequence end.
s.start
integer: subject sequence start.
s.end
integer: subject sequence end.
evalue
numeric: evalue.
bit.score
numeric: score value.
The data was generated with standalone BLAST from NCBI. Pairwise similarities of DNA sequences are calculated among all sequences to analyse applying Standalone Blast with the parameters -m 8 -r 2 -G 5 -E 2.
Alternatively data can be generated with "local BLAST" implemented in BioEdit v7.0.9 using the additional parameters -m 8 -r 2 -G 5 -E 2 and by selecting "open output" and "tabular output".
Standalone Blast download: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Blast News: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
BioEdit: https://bioedit.software.informer.com/
Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.
# NOT RUN {
data(BLASTdata)
str(BLASTdata)
# }
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