R package rMSA - Interface for Popular Multiple Sequence Alignment Tools

Seamlessly interfaces Multiple Sequence Alignment software packages including

• ClustalW
• MAFFT
• MUSCLE
• Kalign
• Boxshade

with the Bioconductor infrastructure. The tools have to be installed separately.

In addition, distances between sets of sequences can be calculated providing.

• k-mer-based distances
  • Jensen-Shannon divergence (JSD) between FFPs (Sims and Kim, 2011)
  • Cosine distance is used between Composition Vectors (Qi et al, 2007)
  • Numerical summarization vector distance (Nagar and Hahsler, 2013)
  • Jaccard distance between sets of k-mers.
  • Distance based on SimRank (Santis et al, 2011)
• Edit distance/alignment-based distances
  • Edit (Levenshtein) Distance (package pwalign)
  • Distance based on alignment scores (package pwalign)
• Evolutionary distances
  • Evolutionary distances (package ape)

A short guide with examples can be found here.

Installation

Current development version: Install from r-universe.

install.packages("rMSA",
    repos = c("https://mhahsler.r-universe.dev". "https://cloud.r-project.org/"))

Additional installation instructions can be found here.

Examples

Align sequences using clustalW.

library("rMSA")

rna <- readRNAStringSet(system.file("examples/RNA_example.fasta", package = "rMSA"))
rna

## RNAStringSet object of length 5:
##     width seq                                               names               
## [1]  1481 AGAGUUUGAUCCUGGCUCAGAAC...GGUGAAGUCGUAACAAGGUAACC 1675 AB015560.1 d...
## [2]  1404 GCUGGCGGCAGGCCUAACACAUG...CACGGUAAGGUCAGCGACUGGGG 4399 D14432.1 Rho...
## [3]  1426 GGAAUGCUNAACACAUGCAAGUC...AACAAGGUAGCCGUAGGGGAACC 4403 X72908.1 Ros...
## [4]  1362 GCUGGCGGAAUGCUUAACACAUG...UACCUUAGGUGUCUAGGCUAACC 4404 AF173825.1 A...
## [5]  1458 AGAGUUUGAUUAUGGCUCAGAGC...UGAAGUCGUAACAAGGUAACCGU 4411 Y07647.2 Dre...

al <- clustal(rna)
al

## RNAMultipleAlignment with 5 rows and 1500 columns
##      aln                                                    names               
## [1] --------------------------...GNAACAAGGUAGCCGUAGGGGAACC 4403
## [2] --------------------------...------------------------- 4404
## [3] AGAGUUUGAUUAUGGCUCAGAGCGAA...GUAACAAGGUAACCGU--------- 4411
## [4] --------------------------...------------------------- 4399
## [5] AGAGUUUGAUCCUGGCUCAGAACGAA...GUAACAAGGUAACC----------- 1675

Cluster mutations of a sequence using SimRank

s <- random_sequences(len = 100, number = 1)
ms <- mutations(s, number = 20)
dSimRank <- distSimRank(ms)
plot(as.dendrogram(hclust(dSimRank)), horiz=TRUE, type="triangle")

How to Cite the Use of this Package

To cite package ‘rMSA’ in publications use:

Hahsler M, Nagar A (2024). rMSA: Interface for Popular Multiple Sequence Alignment Tools. R package version 0.99.1.

@Manual{,
  title = {rMSA: Interface for Popular Multiple Sequence Alignment Tools},
  author = {Michael Hahsler and Anurag Nagar},
  year = {2024},
  note = {R package version 0.99.1},
}

References

Gao, L; Qi, J (2007 Mar 15). “Whole genome molecular phylogeny of large dsDNA viruses using composition vector method.”. BMC evolutionary biology 7: 41. PMID 17359548.

Hahsler M, Nagar A (2024). rMSA: Interface for Popular Multiple Sequence Alignment Tools. R package version 0.99.1.

Anurag Nagar; Michael Hahsler (2013). “Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.” BMC Bioinformatics, 14(Suppl. 11), 2013

Santis et al, Simrank: Rapid and sensitive general-purpose k-mer search tool, BMC Ecology 2011, 11:11

Sims, GE; Kim, SH (2011 May 17). “Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).”. Proceedings of the National Academy of Sciences of the United States of America 108 (20): 8329-34. PMID 21536867.

Qi J, Wang B, Hao B: Whole Proteome Prokaryote Phylogeny without Sequence Alignment: A K-String Composition Approach. Journal of Molecular Evolution 2004, 58:1-11.