BLASTdata: Example data set for BLAST data

Description Usage Format Details Source References Examples

Description

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

Usage

1

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".

Source

The data set was generated by F. Flessa.

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

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Example output

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 ...

RFLPtools documentation built on May 4, 2021, 1:06 a.m.