read.blast: Read BLAST data
In RFLPtools: Tools to analyse RFLP data

Description Usage Arguments Details Value Author(s) References See Also Examples

Function to read BLAST data generated with standalone BLAST from NCBI.

1	read.blast(file, sep = "\t")

`file`	character: BLAST file to read in.
`sep`	the field separator character. Values on each line of the file are separated by this character. Default `"\t"`.

The function reads data which was generated with standalone BLAST from NCBI; see ftp://ftp.ncbi.nih.gov/blast/executables/release/.

Possible steps:
1) Install NCBI BLAST
2) Generate and import database(s)
3) Apply BLAST with options outfmt and out; e.g.
blastn -query Testquery -db Testdatabase -outfmt 6 -out out.txt
or
blastn -query Testquery -db Testdatabase -outfmt 10 -out out.csv
One can also call BLAST from inside R by using function system
system("blastn -query Testquery -db Testdatabase -outfmt 6 -out out.txt")
4) Read in the results
test.res <- read.blast(file = "out.txt")
or
test.res <- read.blast(file = "out.csv", sep = ",")

A data.frame with 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.

Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@botgarten.uni-tuebingen.de,
Matthias Kohl Matthias.Kohl@stamats.de

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

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.

BLASTdata, simMatrix

Dir <- system.file("extdata", package = "RFLPtools") # input directory 
filename <- file.path(Dir, "BLASTexample.txt")
BLAST1 <- read.blast(file = filename)
str(BLAST1)