plot.blast {bio3d} | R Documentation |
Produces a number of basic plots that should facilitate hit selection from the match statistics of a BLAST result.
plot.blast(b, cutoff = 110)
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). |
Examining plots of BLAST alignment lengths, scores, E-values and normalized scores (-log(E-Value)) can aid in the identification sensible hits.
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.
TO BE IMPROVED.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
~~objects to See Also as help
, ~~~
##pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) ) ##blast <- blast.pdb( seq.pdb(pdb), database = "swiss" ) ##ids <- plot.blast( blast ) ##get.seq(ids)