MsaMultipleAlignmentClasses: Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment',...
In msa: Multiple Sequence Alignment
Description
Objects
Details
Methods
Author(s)
References
See Also
Examples
Description
S4 classes for storing multiple alignments of amino
acid, DNA, and RNA sequences along with algorithm metadata
Objects
Objects of these classes are returned by the multiple sequence
alignment algorithms msaClustalW,
msaClustalOmega, msaMuscle, and the
wrapper function msa, all of which are
provided by the msa package.
Details
The class MsaAAMultipleAlignment extends the
AAMultipleAlignment class, the class
MsaDNAMultipleAlignment extends the
DNAMultipleAlignment class, and the class
MsaRNAMultipleAlignment extends the
RNAMultipleAlignment class. All three classes
extend their parent classes by the slots contained in the
MsaMetaData, i.e. all three classes are class
unions of the aforementioned parent classes and the class
MsaMetaData.
Methods
print(x, show=c("alignment", "version", "call"),
showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20, ...):-
prints information about the object x; the show
argument allows for determining what should be printed.
The show must be a character vector and may contain any
combination of the following strings:
if show contains "alignment", the multiple
sequence alignment is printed in a way similar to the
corresponding method from the Biostrings package
(except for the consensus sequence, see below).
If show contains "complete", the entire width of
the alignment is printed by splitting it over multiple blocks of
lines if necessary. This overrules "alignment" if both
are contained in the show argument.
If show contains "version",
the version slot is shown. If show contains
"call", the call slot is shown.
If show contains "standardParams", the
settings of the parameters that are common to all three
multiple sequence alignment algorithms are shown. If show
contains "algParams", the
algorithm-specific parameters are shown.
The order in which the strings are placed in the show
argument does not have an effect on the order in which
data are printed. The default is
show=c("alignment", "version", "call"), i.e. by default,
the multiple sequence alignment is shown along with version and
call information. If show contains "all", the
complete alignment is shown along with version information,
call, and the complete set of parameters.
As said above, by default, printing alignments is similar to
the standard print method provided by the Biostrings
package, whereas including "complete" in the argument
show prints the entire width of the alignment.
Unlike the method from the Biostrings
package, the appearance can be customized: by default,
the consensus sequence is appended below the alignment. To switch
this off, use showConsensus=FALSE. Whether or not sequence
names should be printed can be controlled via the
showNames argument. The width reserved for the sequence
names can be adjusted using the nameWidth argument;
the default is 20 like in the Biostrings method.
If the number of sequences in the alignment is large, output
can become quite lengthy. That is why only the first
halfNrow and the last halfNrow sequences are
shown. To show all sequences, set halfNrow to NA
or -1. Note that print can also handle masked objects,
where the masked sequences/positions are shown as hash marks.
However, the consensus sequences are computed from the
complete, unmasked alignment and displayed as such.
Additional arguments are passed on to
msaConsensusSequence for customizing how the
consensus sequence is computed.
show(object):displays the alignment along with
metadata; synonymous to calling print with default
arguments.
version(object):displays the algorithm with which
the multiple alignment has been computed along with its
version number (see also MsaMetaData).
params(x):accessor to the params slot (see
also MsaMetaData)
Author(s)
Enrico Bonatesta, Christoph Horejs-Kainrath, and
Ulrich Bodenhofer <msa@bioinf.jku.at>
References
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
(2015). msa: an R package for multiple sequence alignment.
Bioinformatics 31(24):3997-3999. DOI:
10.1093/bioinformatics/btv494.
See Also
msa, msaClustalW,
msaClustalOmega, msaMuscle,
MsaMetaData
Examples
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## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
## simple call with default values
myAlignment <- msaClustalOmega(mySeqs)
## show the algorithm version with which the results were created
version(myAlignment)
## show the results
show(myAlignment)
## print the results
print(myAlignment, show="alignment")
print(myAlignment, show="alignment", showConsensus=FALSE)
print(myAlignment, show=c("alignment", "version"))
print(myAlignment, show="standardParams")
print(myAlignment, show="algParams")
print(myAlignment, show=c("call", "version"))
## print results with custom consensus sequence
print(myAlignment, show="complete", type="upperlower", thresh=c(50, 20))
## show the params
params(myAlignment)
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’:
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
using Gonnet
[1] "ClustalOmega 1.2.0"
ClustalOmega 1.2.0
Call:
msaClustalOmega(mySeqs)
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
ClustalOmega 1.2.0
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
Standard params:
gapOpening = default
gapExtension = default
maxiters = 0
verbose = FALSE
Options specific to ClustalOmega 1.2.0:
inputSeqIsFileFlag = FALSE
outputOrder = tree-order
auto = FALSE
dealign = FALSE
force = FALSE
full = FALSE
fullIter = FALSE
isProfile = FALSE
longVersion = FALSE
percentId = FALSE
residueNumber = FALSE
useKimura = FALSE
version = FALSE
ClustalOmega 1.2.0
Call:
msaClustalOmega(mySeqs)
MsaAAMultipleAlignment with 9 rows and 467 columns
aln (1..54) names
[1] MSALVLESRALGRKLSDFGQETSYIEGNSDQN-AVSLIFSLKEEVGALARVLRL PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRL PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAISLIFSLKEEVGALAKVLRL PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAVSLIFSLKEEVGALAKVLRL PH4H_Mus_musculus
[5] ------------------------------------------------------ PH4H_Pseudomonas_...
[6] ------------------------------------------------------ PH4H_Rhizobium_loti
[7] ------------------------------------------------------ PH4H_Caulobacter_...
[8] ------------------------------------------------------ PH4H_Chromobacter...
[9] ------------------------------------------------------ PH4H_Ralstonia_so...
Con ------------------------------------------------------ Consensus
aln (55..108) names
[1] FEENDINLTHIESRPSRLRKDEYEFFTNLDQRSVPALANIIKILRHDIGATVHE PH4H_Bos_taurus
[2] FEENDVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHE PH4H_Homo_sapiens
[3] FEENDINLTHIESRPSRLNKDEYEFFTYLDKRTKPVLGSIIKSLRNDIGATVHE PH4H_Rattus_norve...
[4] FEENEINLTHIESRPSRLNKDEYEFFTYLDKRSKPVLGSIIKSLRNDIGATVHE PH4H_Mus_musculus
[5] ------------------------------------------------------ PH4H_Pseudomonas_...
[6] ------------------------------------------------------ PH4H_Rhizobium_loti
[7] ------------------------------------------------------ PH4H_Caulobacter_...
[8] ------------------------------------------------------ PH4H_Chromobacter...
[9] ------------------------------------------------------ PH4H_Ralstonia_so...
Con ------------------------------------------------------ Consensus
aln (109..162) names
[1] LSRDKKKDTVPWFPRTIQELDNFANQVLSYGAELDADHPGFKDPVYRARRKQFA PH4H_Bos_taurus
[2] LSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Homo_sapiens
[3] LSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Rattus_norve...
[4] LSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Mus_musculus
[5] -----------------------------------------------------M PH4H_Pseudomonas_...
[6] MS--------------V---------------------AEY----ARDCAAQG- PH4H_Rhizobium_loti
[7] ------------------------------------------------MSGDGL PH4H_Caulobacter_...
[8] ----------------------------------MNDRADF---VVPDITTR-- PH4H_Chromobacter...
[9] MA--------------I---------ATPTSAAPTPAPAGFTGTLTDKLREQFA PH4H_Ralstonia_so...
Con .s--------------i---------.....a....d..gf...v.r..r.qfa Consensus
aln (163..216) names
[1] -DIAY---NYRHGQPIPRVEYTEEEKKTWGTVFRTLKSLYKTHACYEHNHIFPL PH4H_Bos_taurus
[2] -DIAY---NYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPL PH4H_Homo_sapiens
[3] -DIAY---NYRHGQPIPRVEYTEEEKQTWGTVFRTLKALYKTHACYEHNHIFPL PH4H_Rattus_norve...
[4] -DIAY---NYRHGQPIPRVEYTEEERKTWGTVFRTLKALYKTHACYEHNHIFPL PH4H_Mus_musculus
[5] KTTQYV---ARQPDDNGFIHYPETEHQVWNTLITRQLKVIEGRACQEYLDGI-- PH4H_Pseudomonas_...
[6] LRGDYSVCRADFTVAQDY-DYSDEEQAVWRTLCDRQTKLTRKLAHHSYLDGV-- PH4H_Rhizobium_loti
[7] SNGPPPGARPDWTIDQGWETYTQAEHDVWITLYERQTDMLHGRACDEFMRGL-- PH4H_Caulobacter_...
[8] KNVGLSHDANDFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGL-- PH4H_Chromobacter...
[9] EGLDGQTLRPDFTMEQPVHRYTAADHATWRTLYDRQEALLPGRACDEFLQGL-- PH4H_Ralstonia_so...
Con ....y.--..r...p.p...yteee..tw.tl..rq..l....ac.e...g.-- Consensus
aln (217..270) names
[1] LEKYCGFREDNIPQLEEVSQFLQSCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Bos_taurus
[2] LEKYCGFHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Homo_sapiens
[3] LEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Rattus_norve...
[4] LEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Mus_musculus
[5] --EQLGLPHERIPQLDEINRVLQATTGWRVARVPALIPFQTFFELLASQQFPVA PH4H_Pseudomonas_...
[6] --EKLGLL-DRIPDFEDVSTKLRKLTGWEIIAVPGLIPAAPFFDHLANRRFPVT PH4H_Rhizobium_loti
[7] --DALDLHRSGIPDFARINEELKRLTGWTVVAVPGLVPDDVFFDHLANRRFPAG PH4H_Caulobacter_...
[8] --ERLEVDADRVPDFNKLNQKLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVT PH4H_Chromobacter...
[9] --STLGMSREGVPSFDRLNETLMRATGWQIVAVPGLVPDEVFFEHLANRRFPAS PH4H_Ralstonia_so...
Con --..lg...d.ipqle.vsq.lq..tgwr...vpgl.p...ff..la.r.fp.t Consensus
aln (271..324) names
[1] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Bos_taurus
[2] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Homo_sapiens
[3] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Rattus_norve...
[4] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Mus_musculus
[5] TFIRTPEELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGKLGLKASKEE-RV PH4H_Pseudomonas_...
[6] NWLRTRQELDYIVEPDMFHDFFGHVPVLSQPVFADFMQMYGKKAGDIIALGGDE PH4H_Rhizobium_loti
[7] QFIRKPHELDYLQEPDIFHDVFGHVPMLTDPVFADYMQAYGEGGRRALGLGRLA PH4H_Caulobacter_...
[8] WWLREPHQLDYLQEPDVFHDLFGHVPLLINPVFADYLEAYGKGGVKAKALGALP PH4H_Chromobacter...
[9] WWMRRPDQLDYLQEPDGFHDIFGHVPLLINPVFADYMQAYGQGGLKAARLGALD PH4H_Ralstonia_so...
Con q.ir....ldy..epdifhelfghvpllsdp.fa.f.q.yg...l.a..e...e Consensus
aln (325..378) names
[1] KLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Bos_taurus
[2] KLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSE-KPKLLPLELEK PH4H_Homo_sapiens
[3] KLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Rattus_norve...
[4] KLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Mus_musculus
[5] FLARLYWMTIEFGLVETD-QGKRIYGGGILSSPKETVYSLSD-EPLHQAFNPLE PH4H_Pseudomonas_...
[6] MITRLYWYTAEYGLVQEAGQPLKAFGAGLMSSFTELQFAVEGKDAHHVPFDLET PH4H_Rhizobium_loti
[7] NLARLYWYTVEFGLMNTP-AGLRIYGAGIVSSRTESIFALDDPSPNRIGFDLER PH4H_Caulobacter_...
[8] MLARLYWYTVEFGLINTP-AGMRIYGAGILSSKSESIYCLDSASPNRVGFDLMR PH4H_Chromobacter...
[9] MLARLYWYTVEFGLIRTP-AGLRIYGAGIVSSKSESVYALDSASPNRIGFDVHR PH4H_Ralstonia_so...
Con .larlyw.tvefgl....-...kaygagllssf.elqyclsd-.p...pf.le. Consensus
aln (379..432) names
[1] TAVQEYTITEFQPLYYVAESFNDAKEKVR--NFAATIPRPFSVH-YDP--YTQR PH4H_Bos_taurus
[2] TAIQNYTVTEFQPLYYVAESFNDAKEKVR--NFAATIPRPFSVR-YDP--YTQR PH4H_Homo_sapiens
[3] TACQEYSVTEFQPLYYVAESFSDAKEKVR--TFAATIPRPFSVR-YDP--YTQR PH4H_Rattus_norve...
[4] TACQEYTVTEFQPLYYVAESFNDAKEKVR--TFAATIPRPFSVR-YDP--YTQR PH4H_Mus_musculus
[5] AMRTPYRIDILQPLYFVLPDLKRLFQLAQ-EDIMALVHEAMRLG-LHAPLFPPK PH4H_Pseudomonas_...
[6] VMRTGYEIDKFQRAYFVLPSFDALRDAFQTADFEAIVARRKDQKALDPATV--- PH4H_Rhizobium_loti
[7] VMRTLYRIDDFQQVYFVIDSIQTLQEVTL-RDFGAIYERLASVSDIGVAEIVPG PH4H_Caulobacter_...
[8] IMNTRYRIDTFQKTYFVIDSFKQLFDATA-PDFAPLYLQLADAQPWGAGDVAPD PH4H_Chromobacter...
[9] IMRTRYRIDTFQKTYFVIDSFEQLFDATR-PDFTPLYEALGTLPTFGAGDVVDG PH4H_Ralstonia_so...
Con .m.t.y.id.fqplyfv..sf..l.e..r-.dfaa...r..sv.-.dp...... Consensus
aln (433..467) names
[1] IEVLDNT-QQLKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] IEVLDNT-QQLKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] VEVLDNT-QQLKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] VEVLDNT-QQLKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] QAA-------------------------------- PH4H_Pseudomonas_...
[6] ----------------------------------- PH4H_Rhizobium_loti
[7] DAVLTRGTQAYATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] DLVLNAGDRQGWADTEDV----------------- PH4H_Chromobacter...
[9] DAVLNAGTREGWADTADI----------------- PH4H_Ralstonia_so...
Con ..vl...-qq...-.ad.......----------- Consensus
$gapOpening
[1] "default"
$gapExtension
[1] "default"
$maxiters
[1] 0
$verbose
[1] FALSE
$inputSeqIsFileFlag
[1] FALSE
$outputOrder
[1] "tree-order"
$auto
[1] FALSE
$dealign
[1] FALSE
$force
[1] FALSE
$full
[1] FALSE
$fullIter
[1] FALSE
$isProfile
[1] FALSE
$longVersion
[1] FALSE
$percentId
[1] FALSE
$residueNumber
[1] FALSE
$useKimura
[1] FALSE
$version
[1] FALSE
msa documentation built on Nov. 8, 2020, 5:41 p.m.
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Description Objects Details Methods Author(s) References See Also Examples
Description
S4 classes for storing multiple alignments of amino acid, DNA, and RNA sequences along with algorithm metadata
Objects
Objects of these classes are returned by the multiple sequence
alignment algorithms msaClustalW,
msaClustalOmega, msaMuscle, and the
wrapper function msa, all of which are
provided by the msa package.
Details
The class MsaAAMultipleAlignment extends the
AAMultipleAlignment class, the class
MsaDNAMultipleAlignment extends the
DNAMultipleAlignment class, and the class
MsaRNAMultipleAlignment extends the
RNAMultipleAlignment class. All three classes
extend their parent classes by the slots contained in the
MsaMetaData, i.e. all three classes are class
unions of the aforementioned parent classes and the class
MsaMetaData.
Methods
print(x, show=c("alignment", "version", "call"), showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20, ...):-
prints information about the object
x; theshowargument allows for determining what should be printed. Theshowmust be a character vector and may contain any combination of the following strings: ifshowcontains"alignment", the multiple sequence alignment is printed in a way similar to the corresponding method from the Biostrings package (except for the consensus sequence, see below). Ifshowcontains"complete", the entire width of the alignment is printed by splitting it over multiple blocks of lines if necessary. This overrules"alignment"if both are contained in theshowargument. Ifshowcontains"version", theversionslot is shown. Ifshowcontains"call", thecallslot is shown. Ifshowcontains"standardParams", the settings of the parameters that are common to all three multiple sequence alignment algorithms are shown. Ifshowcontains"algParams", the algorithm-specific parameters are shown. The order in which the strings are placed in theshowargument does not have an effect on the order in which data are printed. The default isshow=c("alignment", "version", "call"), i.e. by default, the multiple sequence alignment is shown along with version and call information. Ifshowcontains"all", the complete alignment is shown along with version information, call, and the complete set of parameters. As said above, by default, printing alignments is similar to the standardprintmethod provided by the Biostrings package, whereas including"complete"in the argumentshowprints the entire width of the alignment. Unlike the method from the Biostrings package, the appearance can be customized: by default, the consensus sequence is appended below the alignment. To switch this off, useshowConsensus=FALSE. Whether or not sequence names should be printed can be controlled via theshowNamesargument. The width reserved for the sequence names can be adjusted using thenameWidthargument; the default is 20 like in the Biostrings method. If the number of sequences in the alignment is large, output can become quite lengthy. That is why only the firsthalfNrowand the lasthalfNrowsequences are shown. To show all sequences, sethalfNrowtoNAor -1. Note thatprintcan also handle masked objects, where the masked sequences/positions are shown as hash marks. However, the consensus sequences are computed from the complete, unmasked alignment and displayed as such. Additional arguments are passed on tomsaConsensusSequencefor customizing how the consensus sequence is computed. show(object):displays the alignment along with metadata; synonymous to calling
printwith default arguments.version(object):displays the algorithm with which the multiple alignment has been computed along with its version number (see also
MsaMetaData).params(x):accessor to the
paramsslot (see alsoMsaMetaData)
Author(s)
Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <msa@bioinf.jku.at>
References
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.
See Also
msa, msaClustalW,
msaClustalOmega, msaMuscle,
MsaMetaData
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
## simple call with default values
myAlignment <- msaClustalOmega(mySeqs)
## show the algorithm version with which the results were created
version(myAlignment)
## show the results
show(myAlignment)
## print the results
print(myAlignment, show="alignment")
print(myAlignment, show="alignment", showConsensus=FALSE)
print(myAlignment, show=c("alignment", "version"))
print(myAlignment, show="standardParams")
print(myAlignment, show="algParams")
print(myAlignment, show=c("call", "version"))
## print results with custom consensus sequence
print(myAlignment, show="complete", type="upperlower", thresh=c(50, 20))
## show the params
params(myAlignment)
|
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’:
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
using Gonnet
[1] "ClustalOmega 1.2.0"
ClustalOmega 1.2.0
Call:
msaClustalOmega(mySeqs)
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
ClustalOmega 1.2.0
MsaAAMultipleAlignment with 9 rows and 467 columns
aln names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus
Standard params:
gapOpening = default
gapExtension = default
maxiters = 0
verbose = FALSE
Options specific to ClustalOmega 1.2.0:
inputSeqIsFileFlag = FALSE
outputOrder = tree-order
auto = FALSE
dealign = FALSE
force = FALSE
full = FALSE
fullIter = FALSE
isProfile = FALSE
longVersion = FALSE
percentId = FALSE
residueNumber = FALSE
useKimura = FALSE
version = FALSE
ClustalOmega 1.2.0
Call:
msaClustalOmega(mySeqs)
MsaAAMultipleAlignment with 9 rows and 467 columns
aln (1..54) names
[1] MSALVLESRALGRKLSDFGQETSYIEGNSDQN-AVSLIFSLKEEVGALARVLRL PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRL PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAISLIFSLKEEVGALAKVLRL PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAVSLIFSLKEEVGALAKVLRL PH4H_Mus_musculus
[5] ------------------------------------------------------ PH4H_Pseudomonas_...
[6] ------------------------------------------------------ PH4H_Rhizobium_loti
[7] ------------------------------------------------------ PH4H_Caulobacter_...
[8] ------------------------------------------------------ PH4H_Chromobacter...
[9] ------------------------------------------------------ PH4H_Ralstonia_so...
Con ------------------------------------------------------ Consensus
aln (55..108) names
[1] FEENDINLTHIESRPSRLRKDEYEFFTNLDQRSVPALANIIKILRHDIGATVHE PH4H_Bos_taurus
[2] FEENDVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHE PH4H_Homo_sapiens
[3] FEENDINLTHIESRPSRLNKDEYEFFTYLDKRTKPVLGSIIKSLRNDIGATVHE PH4H_Rattus_norve...
[4] FEENEINLTHIESRPSRLNKDEYEFFTYLDKRSKPVLGSIIKSLRNDIGATVHE PH4H_Mus_musculus
[5] ------------------------------------------------------ PH4H_Pseudomonas_...
[6] ------------------------------------------------------ PH4H_Rhizobium_loti
[7] ------------------------------------------------------ PH4H_Caulobacter_...
[8] ------------------------------------------------------ PH4H_Chromobacter...
[9] ------------------------------------------------------ PH4H_Ralstonia_so...
Con ------------------------------------------------------ Consensus
aln (109..162) names
[1] LSRDKKKDTVPWFPRTIQELDNFANQVLSYGAELDADHPGFKDPVYRARRKQFA PH4H_Bos_taurus
[2] LSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Homo_sapiens
[3] LSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Rattus_norve...
[4] LSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFA PH4H_Mus_musculus
[5] -----------------------------------------------------M PH4H_Pseudomonas_...
[6] MS--------------V---------------------AEY----ARDCAAQG- PH4H_Rhizobium_loti
[7] ------------------------------------------------MSGDGL PH4H_Caulobacter_...
[8] ----------------------------------MNDRADF---VVPDITTR-- PH4H_Chromobacter...
[9] MA--------------I---------ATPTSAAPTPAPAGFTGTLTDKLREQFA PH4H_Ralstonia_so...
Con .s--------------i---------.....a....d..gf...v.r..r.qfa Consensus
aln (163..216) names
[1] -DIAY---NYRHGQPIPRVEYTEEEKKTWGTVFRTLKSLYKTHACYEHNHIFPL PH4H_Bos_taurus
[2] -DIAY---NYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPL PH4H_Homo_sapiens
[3] -DIAY---NYRHGQPIPRVEYTEEEKQTWGTVFRTLKALYKTHACYEHNHIFPL PH4H_Rattus_norve...
[4] -DIAY---NYRHGQPIPRVEYTEEERKTWGTVFRTLKALYKTHACYEHNHIFPL PH4H_Mus_musculus
[5] KTTQYV---ARQPDDNGFIHYPETEHQVWNTLITRQLKVIEGRACQEYLDGI-- PH4H_Pseudomonas_...
[6] LRGDYSVCRADFTVAQDY-DYSDEEQAVWRTLCDRQTKLTRKLAHHSYLDGV-- PH4H_Rhizobium_loti
[7] SNGPPPGARPDWTIDQGWETYTQAEHDVWITLYERQTDMLHGRACDEFMRGL-- PH4H_Caulobacter_...
[8] KNVGLSHDANDFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGL-- PH4H_Chromobacter...
[9] EGLDGQTLRPDFTMEQPVHRYTAADHATWRTLYDRQEALLPGRACDEFLQGL-- PH4H_Ralstonia_so...
Con ....y.--..r...p.p...yteee..tw.tl..rq..l....ac.e...g.-- Consensus
aln (217..270) names
[1] LEKYCGFREDNIPQLEEVSQFLQSCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Bos_taurus
[2] LEKYCGFHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Homo_sapiens
[3] LEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Rattus_norve...
[4] LEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCT PH4H_Mus_musculus
[5] --EQLGLPHERIPQLDEINRVLQATTGWRVARVPALIPFQTFFELLASQQFPVA PH4H_Pseudomonas_...
[6] --EKLGLL-DRIPDFEDVSTKLRKLTGWEIIAVPGLIPAAPFFDHLANRRFPVT PH4H_Rhizobium_loti
[7] --DALDLHRSGIPDFARINEELKRLTGWTVVAVPGLVPDDVFFDHLANRRFPAG PH4H_Caulobacter_...
[8] --ERLEVDADRVPDFNKLNQKLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVT PH4H_Chromobacter...
[9] --STLGMSREGVPSFDRLNETLMRATGWQIVAVPGLVPDEVFFEHLANRRFPAS PH4H_Ralstonia_so...
Con --..lg...d.ipqle.vsq.lq..tgwr...vpgl.p...ff..la.r.fp.t Consensus
aln (271..324) names
[1] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Bos_taurus
[2] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Homo_sapiens
[3] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Rattus_norve...
[4] QYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDE-YIE PH4H_Mus_musculus
[5] TFIRTPEELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGKLGLKASKEE-RV PH4H_Pseudomonas_...
[6] NWLRTRQELDYIVEPDMFHDFFGHVPVLSQPVFADFMQMYGKKAGDIIALGGDE PH4H_Rhizobium_loti
[7] QFIRKPHELDYLQEPDIFHDVFGHVPMLTDPVFADYMQAYGEGGRRALGLGRLA PH4H_Caulobacter_...
[8] WWLREPHQLDYLQEPDVFHDLFGHVPLLINPVFADYLEAYGKGGVKAKALGALP PH4H_Chromobacter...
[9] WWMRRPDQLDYLQEPDGFHDIFGHVPLLINPVFADYMQAYGQGGLKAARLGALD PH4H_Ralstonia_so...
Con q.ir....ldy..epdifhelfghvpllsdp.fa.f.q.yg...l.a..e...e Consensus
aln (325..378) names
[1] KLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Bos_taurus
[2] KLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSE-KPKLLPLELEK PH4H_Homo_sapiens
[3] KLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Rattus_norve...
[4] KLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEK PH4H_Mus_musculus
[5] FLARLYWMTIEFGLVETD-QGKRIYGGGILSSPKETVYSLSD-EPLHQAFNPLE PH4H_Pseudomonas_...
[6] MITRLYWYTAEYGLVQEAGQPLKAFGAGLMSSFTELQFAVEGKDAHHVPFDLET PH4H_Rhizobium_loti
[7] NLARLYWYTVEFGLMNTP-AGLRIYGAGIVSSRTESIFALDDPSPNRIGFDLER PH4H_Caulobacter_...
[8] MLARLYWYTVEFGLINTP-AGMRIYGAGILSSKSESIYCLDSASPNRVGFDLMR PH4H_Chromobacter...
[9] MLARLYWYTVEFGLIRTP-AGLRIYGAGIVSSKSESVYALDSASPNRIGFDVHR PH4H_Ralstonia_so...
Con .larlyw.tvefgl....-...kaygagllssf.elqyclsd-.p...pf.le. Consensus
aln (379..432) names
[1] TAVQEYTITEFQPLYYVAESFNDAKEKVR--NFAATIPRPFSVH-YDP--YTQR PH4H_Bos_taurus
[2] TAIQNYTVTEFQPLYYVAESFNDAKEKVR--NFAATIPRPFSVR-YDP--YTQR PH4H_Homo_sapiens
[3] TACQEYSVTEFQPLYYVAESFSDAKEKVR--TFAATIPRPFSVR-YDP--YTQR PH4H_Rattus_norve...
[4] TACQEYTVTEFQPLYYVAESFNDAKEKVR--TFAATIPRPFSVR-YDP--YTQR PH4H_Mus_musculus
[5] AMRTPYRIDILQPLYFVLPDLKRLFQLAQ-EDIMALVHEAMRLG-LHAPLFPPK PH4H_Pseudomonas_...
[6] VMRTGYEIDKFQRAYFVLPSFDALRDAFQTADFEAIVARRKDQKALDPATV--- PH4H_Rhizobium_loti
[7] VMRTLYRIDDFQQVYFVIDSIQTLQEVTL-RDFGAIYERLASVSDIGVAEIVPG PH4H_Caulobacter_...
[8] IMNTRYRIDTFQKTYFVIDSFKQLFDATA-PDFAPLYLQLADAQPWGAGDVAPD PH4H_Chromobacter...
[9] IMRTRYRIDTFQKTYFVIDSFEQLFDATR-PDFTPLYEALGTLPTFGAGDVVDG PH4H_Ralstonia_so...
Con .m.t.y.id.fqplyfv..sf..l.e..r-.dfaa...r..sv.-.dp...... Consensus
aln (433..467) names
[1] IEVLDNT-QQLKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] IEVLDNT-QQLKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] VEVLDNT-QQLKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] VEVLDNT-QQLKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] QAA-------------------------------- PH4H_Pseudomonas_...
[6] ----------------------------------- PH4H_Rhizobium_loti
[7] DAVLTRGTQAYATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] DLVLNAGDRQGWADTEDV----------------- PH4H_Chromobacter...
[9] DAVLNAGTREGWADTADI----------------- PH4H_Ralstonia_so...
Con ..vl...-qq...-.ad.......----------- Consensus
$gapOpening
[1] "default"
$gapExtension
[1] "default"
$maxiters
[1] 0
$verbose
[1] FALSE
$inputSeqIsFileFlag
[1] FALSE
$outputOrder
[1] "tree-order"
$auto
[1] FALSE
$dealign
[1] FALSE
$force
[1] FALSE
$full
[1] FALSE
$fullIter
[1] FALSE
$isProfile
[1] FALSE
$longVersion
[1] FALSE
$percentId
[1] FALSE
$residueNumber
[1] FALSE
$useKimura
[1] FALSE
$version
[1] FALSE
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