pid {Biostrings} | R Documentation |
Calculates the percent sequence identity for a pairwise sequence alignment.
pid(x, type="PID1")
x |
a PairwiseAlignedXStringSet object. |
type |
one of percent sequence identity. One of "PID1" , "PID2" ,
"PID3" , and "PID4" . See Details for more information. |
Since there is no universal definition of percent sequence identity, the pid
function
calculates this statistic in the following types:
"PID1"
:"PID2"
:"PID3"
:"PID4"
:A numeric vector containing the specified sequence identity measures.
P. Aboyoun
A. May, Percent Sequence Identity: The Need to Be Explicit, Structure 2004, 12(5):737.
G. Raghava and G. Barton, Quantification of the variation in percentage identity for protein sequence alignments, BMC Bioinformatics 2006, 7:415.
pairwiseAlignment, PairwiseAlignedXStringSet-class, match-utils
s1 <- DNAString("AGTATAGATGATAGAT") s2 <- DNAString("AGTAGATAGATGGATGATAGATA") palign1 <- pairwiseAlignment(s1, s2) palign1 pid(palign1) palign2 <- pairwiseAlignment(s1, s2, substitutionMatrix = nucleotideSubstitutionMatrix(match = 2, mismatch = 10, baseOnly = TRUE)) palign2 pid(palign2, type = "PID4")