AdjustAlignment: Improve An Existing Alignment By Adjusting Gap Placements

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Makes small adjustments by shifting groups of gaps left and right to find their optimal positioning in a multiple sequence alignment.

Usage

AdjustAlignment(myXStringSet,
                perfectMatch = 5,
                misMatch = 0,
                gapLetter = -3,
                gapOpening = -0.1,
                gapExtension = 0,
                substitutionMatrix = NULL,
                shiftPenalty = -0.2,
                threshold = 0.1,
                weight = 1,
                processors = 1)

Arguments

myXStringSet	An AAStringSet, DNAStringSet, or RNAStringSet object of aligned sequences.
perfectMatch	Numeric giving the reward for aligning two matching nucleotides in the alignment. Only used for DNAStringSet or RNAStringSet inputs.
misMatch	Numeric giving the cost for aligning two mismatched nucleotides in the alignment. Only used for DNAStringSet or RNAStringSet inputs.
gapLetter	Numeric giving the cost for aligning gaps to letters. A lower value (more negative) encourages the overlapping of gaps across different sequences in the alignment.
gapOpening	Numeric giving the cost for opening or closing a gap in the alignment.
gapExtension	Numeric giving the cost for extending an open gap in the alignment.
substitutionMatrix	Either a substitution matrix representing the substitution scores for an alignment or the name of the amino acid substitution matrix to use in alignment. The latter may be one of the following: “BLOSUM45”, “BLOSUM50”, “BLOSUM62”, “BLOSUM80”, “BLOSUM100”, “PAM30”, “PAM40”, “PAM70”, “PAM120”, “PAM250”, or “MIQS”. The default (NULL) will use the perfectMatch and misMatch penalties for DNA/RNA or PFASUM50 for AA.
shiftPenalty	Numeric giving the cost for every additional position that a group of gaps is shifted.
threshold	Numeric specifying the improvement in score required to permanently apply an adjustment to the alignment.
weight	A numeric vector of weights for each sequence, or a single number implying equal weights.
processors	The number of processors to use, or NULL to automatically detect and use all available processors.

Details

The process of multiple sequence alignment often results in the integration of small imperfections into the final alignment. Some of these errors are obvious by-eye, which encourages manual refinement of automatically generated alignments. However, the manual refinement process is inherently subjective and time consuming. AdjustAlignment refines an existing alignment in a process similar to that which might be applied manually, but in a repeatable and must faster fashion. This function shifts all of the gaps in an alignment to the left and right to find their optimal positioning. The optimal position is defined as the position that maximizes the alignment “score”, which is determined by the input parameters. The resulting alignment will be similar to the input alignment but with many imperfections eliminated. Note that the affine gap penalties here are different from the more flexible penalties used in AlignProfiles, and have been optimized independently.

Value

An XStringSet of aligned sequences.

Author(s)

Erik Wright [e-mail]

References

Wright, E. S. (2015). DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics, 16, 322. http://doi.org/10.1186/s12859-015-0749-z

Wright, E. S. (2020). RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. RNA 2020, 26, 531-540.

See Also

AlignSeqs, AlignTranslation, PFASUM, StaggerAlignment

Examples

# a trivial example
aa <- AAStringSet(c("ARN-PK", "ARRP-K"))
aa # input alignment
AdjustAlignment(aa) # output alignment

# specifying an alternative substitution matrix
AdjustAlignment(aa, substitutionMatrix="BLOSUM62")

# a real example
fas <- system.file("extdata", "Streptomyces_ITS_aligned.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
dna # input alignment
adjustedDNA <- AdjustAlignment(dna) # output alignment
BrowseSeqs(adjustedDNA, highlight=1)
adjustedDNA==dna # most sequences were adjusted (those marked FALSE)

Example output

Loading required package: Biostrings
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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

Loading required package: RSQLite
  A AAStringSet instance of length 2
    width seq
[1]     6 ARN-PK
[2]     6 ARRP-K
  A AAStringSet instance of length 2
    width seq
[1]     5 ARNPK
[2]     5 ARRPK
  A AAStringSet instance of length 2
    width seq
[1]     5 ARNPK
[2]     5 ARRPK
  A DNAStringSet instance of length 88
     width seq                                              names               
 [1]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC supercont3.1 of S...
 [2]   627 NNNNCACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC supercont3.1 of S...
 [3]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC supercont1.1 of S...
 [4]   627 CGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC supercont1.1 of S...
 [5]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC supercont1.1 of S...
 ...   ... ...
[84]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC gi|297189896|ref|...
[85]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTGTCCGAATGGGGAAACC gi|224581106|ref|...
[86]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTGTCCGAATGGGGAAACC gi|224581106|ref|...
[87]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTGTCCGAATGGGGAAACC gi|224581106|ref|...
[88]   627 TGTACACACCGCCCGTCA-CGTC...GGGGTTTCCGAATGGGGAAACC gi|224581108|ref|...
 [1] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[37] FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
[49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[85] FALSE FALSE FALSE FALSE

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.