Interface to Popular Multiple Sequence Alignment Tools - R-package
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README.md

rMSA - Interface for Popular Multiple Sequence Alignment Tools (R package)

Travis-CI Build Status AppVeyor Build Status

Seamlessly interfaces Multiple Sequence Alignment software packages including ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) with the Bioconductor infrastructure. A short guide with examples can be found here.

Installation

  • Install Bioconductor and the Bioconductor packages Biostrings and seqLogo.
  • Download and install the package from AppVeyor or install via intall_github("mhahsler/rMSA") (needs devtools)
  • To install individual MSA tools follow the instructions found in ? rMSA_INSTALL

Example

R> library("rMSA")

R> rna <- readRNAStringSet(system.file("examples/RNA_example.fasta", package="rMSA"))
R> rna
  A RNAStringSet instance of length 5
    width seq                                                                    names               
[1]  1481 AGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCG...UGGUGAUCGGGGUGAAGUCGUAACAAGGUAACC 1675 AB015560.1 d...
[2]  1404 GCUGGCGGCAGGCCUAACACAUGCAAGUCGAACG...GGCAGCCGACCACGGUAAGGUCAGCGACUGGGG 4399 D14432.1 Rho...
[3]  1426 GGAAUGCUNAACACAUGCAAGUCGCACGGGCAGC...GUGUAGUCGNAACAAGGUAGCCGUAGGGGAACC 4403 X72908.1 Ros...
[4]  1362 GCUGGCGGAAUGCUUAACACAUGCAAGUCGCACG...GAGUUGGUUUUACCUUAGGUGUCUAGGCUAACC 4404 AF173825.1 A...
[5]  1458 AGAGUUUGAUUAUGGCUCAGAGCGAACGCUGGCG...GCGACUGGGGUGAAGUCGUAACAAGGUAACCGU 4411 Y07647.2 Dre...

R> al <- clustal(rna)
Alignment Score 71657

R> al
RNAMultipleAlignment with 5 rows and 1500 columns
     aln                                                                         names               
[1] ---------------------------------GGA...GGGGUGUAGUCGNAACAAGGUAGCCGUAGGGGAACC 4403
[2] ---------------------------GCUGGCGGA...------------------------------------ 4404
[3] AGAGUUUGAUUAUGGCUCAGAGCGAACGCUGGCGGC...GGGGUGAAGUCGUAACAAGGUAACCGU--------- 4411
[4] ---------------------------GCUGGCGGC...GGGG-------------------------------- 4399
[5] AGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGC...GGGGUGAAGUCGUAACAAGGUAACC----------- 1675