# Percent Sequence Identity

### Description

Calculates the percent sequence identity for a pairwise sequence alignment.

### Usage

1 | ```
pid(x, type="PID1")
``` |

### Arguments

`x` |
a |

`type` |
one of percent sequence identity. One of |

### 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

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
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")
``` |

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