plot.blast {bio3d}R Documentation

Plot BLAST Hit Statistics.

Description

Produces a number of basic plots that should facilitate hit selection from the match statistics of a BLAST result.

Usage

plot.blast(b, cutoff = 110)

Arguments

b BLAST results as obtained from the function blast.pdb.
cutoff A cutoff value, in terms of minus the log of the evalue, for returned hits (see below).

Details

Examining plots of BLAST alignment lengths, scores, E-values and normalized scores (-log(E-Value)) can aid in the identification sensible hits.

Value

Produces a plot on the active graphics device and returns a matrix with the PDB and GI identifiers of the subset of hits with a normalized score above the chosen cutoff.

Note

TO BE IMPROVED.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

~~objects to See Also as help, ~~~

Examples

##pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) )
##blast <- blast.pdb( seq.pdb(pdb), database = "swiss" )
##ids <- plot.blast( blast )
##get.seq(ids)

[Package bio3d version 1.0-6 Index]