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.
Biostrings
and seqLogo
.install_github("mhahsler/rMSA")
(needs devtools) ? rMSA_INSTALL
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
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