In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

pkg <- "rMSA"

source("https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R")
pkg_title(pkg, CRAN = FALSE)

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.

pkg_install(pkg, CRAN = FALSE)

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

al <- clustal(rna)
al

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

pkg_citation(pkg)

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.

mhahsler/rMSA documentation built on May 24, 2024, 3:36 p.m.