Description Details Author(s) References See Also Examples
The msa package provides a unified R/Bioconductor interface to different multiple sequence alignment algorithms. Currently, ‘ClustalW’, ‘ClustalOmega’, and ‘MUSCLE’ are supported. All algorithms are usable without additional software packages and on all major platforms. The multiple sequence algorithms are complemented by an R interface to the powerful LaTeX package texshade.sty which allows for a highly customizable plots of multiple sequence alignments.
Package: | msa |
Type: | Package |
Version: | 1.1.2 |
Date: | 2015-09-29 |
License: | GPL-2 |
Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <msa@bioinf.jku.at>
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.
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-4680. DOI: 10.1093/nar/22.22.4673.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D., and Higgins, D. G. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539. DOI: 10.1038/msb.2011.75.
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. DOI: 10.1093/nar/gkh340.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. DOI: 10.1186/1471-2105-5-113.
Beitz, E. (2000) TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e Bioinformatics 16(2):135-139. DOI: 10.1093/bioinformatics/16.2.135.
msa
, msaClustalW
,
msaClustalOmega
, msaMuscle
,
msaPrettyPrint
1 2 3 4 5 6 7 | ## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
## call unified interface msa() for default method (ClustalW) and
## default parameters
msa(mySeqs)
|
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
use default substitution matrix
CLUSTAL 2.1
Call:
msa(mySeqs)
MsaAAMultipleAlignment with 9 rows and 456 columns
aln names
[1] MAAVVLENGVLSRKLSDFGQETSYIE...QLKILADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[2] MAAVVLENGVLSRKLSDFGQETSYIE...QLKILADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[3] MSTAVLENPGLGRKLSDFGQETSYIE...QLKILADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[4] MSALVLESRALGRKLSDFGQETSYIE...QLKILADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[5] --------------------------...LNAGDRQGWADTEDV---------- PH4H_Chromobacter...
[6] --------------------------...LNAGTREGWADTADI---------- PH4H_Ralstonia_so...
[7] --------------------------...LTRGT-QAYATAGGRLAGAAAG--- PH4H_Caulobacter_...
[8] --------------------------...------------------------- PH4H_Pseudomonas_...
[9] --------------------------...------------------------- PH4H_Rhizobium_loti
Con --------------------------...??????????????IL??A???--- Consensus
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