QualityAlignedXStringSet classes are
containers for storing an aligned
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:
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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:
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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.
In the code snippets below,
x is a
The original string.
aligned(x, degap = FALSE):
degap = FALSE, the "filled-with-gaps subsequence" representing
the aligned substring. If
degap = TRUE, the "gap-less subsequence"
representing the aligned substring.
ranges(x): The bounds of the aligned substring.
The start of the aligned substring.
The end of the aligned substring.
The width of the aligned substring, ignoring gaps.
The positions, in the form of an
IRanges object, of the insertions or
deletions (depending on what
A two-column matrix containing the length and sum of the widths for each of
the elements returned by
The length of the
The nchar of the
aligned(x) to a character vector.
Returns a new
object made of the selected elements.
Returns a new
object made of the repeated elements.
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pattern <- AAString("LAND") subject <- AAString("LEAVES") pa1 <- pairwiseAlignment(pattern, subject, substitutionMatrix="BLOSUM50", gapOpening=3, gapExtension=1) alignedPattern <- pattern(pa1) class(alignedPattern) # AlignedXStringSet object unaligned(alignedPattern) aligned(alignedPattern) as.character(alignedPattern) nchar(alignedPattern)
Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit  "AlignedXStringSet" attr(,"package")  "Biostrings" AAStringSet object of length 1: width seq  4 LAND AAStringSet object of length 1: width seq  6 L-A-ND  "L-A-ND"  6
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