Description Usage Format Details Source References Examples
This is an example data set for BLAST data generated with standalone BLAST from NCBI.
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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".
The data set was generated by F. Flessa.
Standalone Blast download: ftp://ftp.ncbi.nih.gov/blast/executables/release/
Blast News: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
BioEdit v7.0.9: Tom Hall, Ibis Biosciences; http://www.mbio.ncsu.edu/BioEdit/bioedit.html
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.
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Loading required package: RColorBrewer
'data.frame': 4069 obs. of 12 variables:
$ query.id : chr "agrFF002" "agrFF002" "agrFF002" "agrFF002" ...
$ subject.id : chr "agrFF002" "agrFF148" "agrFF148" "agrFF176" ...
$ identity : num 100 93.4 100 91.4 100 ...
$ alignment.length: int 544 243 11 255 11 255 11 256 11 256 ...
$ mismatches : int 0 14 0 20 0 20 0 18 0 18 ...
$ gap.opens : int 0 2 0 2 0 2 0 3 0 3 ...
$ q.start : int 1 199 462 187 462 187 462 187 462 187 ...
$ q.end : int 544 439 472 439 472 439 472 439 472 439 ...
$ s.start : int 1 671 785 123 250 121 248 121 248 126 ...
$ s.end : int 544 913 795 377 260 375 258 375 258 380 ...
$ evalue : num 0.0 6.0e-102 6.7 2.0e-100 6.7 ...
$ bit.score : num 944 360 21.1 354 21.1 354 21.1 352 21.1 352 ...
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