PairwiseAlignedFixedSubject-class {Biostrings}R Documentation

PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects

Description

The PairwiseAlignedFixedSubject class is a container for storing an alignment. The PairwiseAlignedFixedSubjectSummary class is a container for storing the summary of an alignment.

Details

Before we define the notion of alignment, we introduce the notion of "filled-with-gaps subsequence". A "filled-with-gaps subsequence" of a string string1 is obtained by inserting 0 or any number of gaps in a subsequence of s1. For example L-A–ND and A–N-D are "filled-with-gaps subsequences" of LAND. An alignment between two strings string1 and string2 results in two strings (align1 and align2) that have the same length and are "filled-with-gaps subsequences" of string1 and string2.

For example, this is an alignment between LAND and LEAVES:

    L-A
    LEA

An alignment can be seen as a compact representation of one set of basic operations that transforms string1 into align1. There are 3 different kinds of basic operations: "insertions" (gaps in align1), "deletions" (gaps in align2), "replacements". The above alignment represents the following basic operations:

    insert E at pos 2
    insert V at pos 4
    insert E at pos 5
    replace by S at pos 6 (N is replaced by S)
    delete at pos 7 (D is deleted)
Note that "insert X at pos i" means that all letters at a position >= i are moved 1 place to the right before X is actually inserted.

There are many possible alignments between two given strings string1 and string2 and a common problem is to find the one (or those ones) with the highest score, i.e. with the lower total cost in terms of basic operations.

Accesor methods

In the code snippets below, x is a PairwiseAlignedFixedSubject object, except otherwise noted.

pattern(x): The AlignedXStringSet object for the pattern.
subject(x): The AlignedXStringSet object for the subject.
type(x): The type of the alignment ("global", "local", "overlap", "patternOverlap", or "subjectOverlap"). There is a method for PairwiseAlignedFixedSubjectSummary as well.
score(x): The score of the alignment (integer). There is a method for PairwiseAlignedFixedSubjectSummary as well.
nindel(x): An InDel object containing the number of insertions and deletions.
length(x): The length of the aligned(pattern(x)) and aligned(subject(x)). There is a method for PairwiseAlignedFixedSubjectSummary as well.
nchar(x): The nchar of the aligned(pattern(x)) and aligned(subject(x)). There is a method for PairwiseAlignedFixedSubjectSummary as well.
alphabet(x): Equivalent to alphabet(unaligned(subject(x))).
summary(object, ...): Generates a summary for the PairwiseAlignedFixedSubject.
aligned(x): Returns an XStringSet object containing the aligned patterns without insertions. This operation ``aligns" the alignments.
as.character(x): Converts aligned(x) to a character vector.
as.matrix(x): Returns an "exploded" character matrix representation of aligned(x).
Views(subject, start=NA, end=NA, names=NULL): The XStringViews object that represents the pairwise alignments along unaligned(subject(subject)). The start and end arguments must be either NA or an integer vector of length 1 that denotes the offset from start(subject(subject)).
toString(x): Equivalent to toString(as.character(x)).

Subsetting methods

x[i]: Returns a new PairwiseAlignedFixedSubject object made of the selected elements.
rep(x, times): Returns a new PairwiseAlignedFixedSubject object made of the repeated elements.

Author(s)

P. Aboyoun and H. Pages

See Also

pairwiseAlignment, AlignedXStringSet-class, XString-class, XStringViews-class, match-utils

Examples

  pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
  subject <- AAString("SMDDTEKMSMKL")
  nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50", gapOpening = -3, gapExtension = -1)
  pattern(nw1)
  subject(nw1)
  aligned(nw1)
  as.character(nw1)
  as.matrix(nw1)
  nchar(nw1)
  score(nw1)
  nw1

[Package Biostrings version 2.10.22 Index]