pid                package:Biostrings                R Documentation

Percent Sequence Identity

Description:

     Calculates the percent sequence identity for a pairwise sequence
     alignment.

Usage:

     pid(x, type="PID1")

Arguments:

       x: a 'PairwiseAlignedXStringSet' object.

    type: one of percent sequence identity. One of '"PID1"', '"PID2"',
          '"PID3"', and '"PID4"'. See Details for more information.

Details:

     Since there is no universal definition of percent sequence
     identity, the 'pid' function calculates this statistic in the
     following types:

     '"PID1"': 100 * (identical positions) / (aligned positions +
          internal gap positions)

     '"PID2"': 100 * (identical positions) / (aligned positions)

     '"PID3"': 100 * (identical positions) / (length shorter sequence)

     '"PID4"': 100 * (identical positions) / (average length of the two
          sequences)


Value:

     A numeric vector containing the specified sequence identity
     measures.

Author(s):

     P. Aboyoun

References:

     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.

See Also:

     pairwiseAlignment, PairwiseAlignedXStringSet-class, match-utils

Examples:

       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")

