RFLPtools (version 2.0)

BLASTdata: Example data set for BLAST data

Description

This is an example data set for BLAST data generated with standalone BLAST from NCBI.

Usage

data(RFLPdata)

Format

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.

Details

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".

References

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.

Examples

# NOT RUN {
data(BLASTdata)
str(BLASTdata)
# }