pid {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 `PairwiseAlignments` 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, PairwiseAlignments-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")

[Package Biostrings version 2.56.0 Index]