Package 'rMSA'

Title: Interface for Popular Multiple Sequence Alignment Tools
Description: Seamlessly interfaces the Multiple Sequence Alignment software packages ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) and provides support to calcualte distances between sequences. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
Authors: Michael Hahsler, Anurag Nagar
Maintainer: Michael Hahsler <[email protected]>
License: GPL-3
Version: 0.99.1
Built: 2024-12-19 04:37:41 UTC
Source: https://github.com/mhahsler/rMSA

Help Index


Boxshade: Shading Multiple Aligned Sequences

Description

Executes boxshade on a multiple sequence alignment.

Usage

boxshade(x, file, dev="pdf", param="-thr=0.5 -cons -def",
    pdfCrop=TRUE)
boxshade_help()

Arguments

x

a multiple alignment as an object of class DNAMultipleAlignment, RNAMultipleAlignment or AAMultipleAlignment.

file

output file

dev

used output device. Available are: ps, eps, hpgl, rtf, crt, ansi, vt, ascii, fig, pict, html and pdf.

param

character string with the command line parameters for clustal (see output of boxshade_help()).

pdfCrop

crop the pdf file if it is smaller than a page. Use FALSE if you want the results on a page or the alignment covers multiple pages.

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

Only a file is created.

Author(s)

Michael Hahsler

References

Boxshade has been written by Kay Hofmann and Michael D. Baron

Examples

## Not run: 
rna <- readRNAStringSet(system.file("examples/RNA_example.fasta",
	package="rMSA"))
rna <- narrow(rna, start=1, end=50)

al <- clustal(rna)

boxshade(al, file="alignment.pdf", dev="pdf")

## End(Not run)

Run Multiple Sequence Alignment (ClustalW) on a Set of Sequences

Description

Executes Clustal on a set of sequences to obtain a multiple sequence alignment.

Usage

clustal(x, param)
clustal_help()

Arguments

x

an object of class XStringSet (e.g., DNAStringSet) with the sequences to be aligned.

param

character string with the command line parameters for clustal (see output of clustal_help()).

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

An object of class DNAMultipleAlignment (see BioStrings).

Author(s)

Michael Hahsler

References

Larkin M., et al. Clustal W and Clustal X version 2.0, Bioinformatics 2007 23(21):2947-29

Examples

## Not run: 
### DNA
dna <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
dna

al <- clustal(dna)
al

### inspect alignment
detail(al)

### plot a sequence logo for the first 20 positions
plot(al, 1, 20)

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

al <- clustal(rna)
al

### Proteins
aa <- readAAStringSet(system.file("examples/Protein_example.fasta",
	package="rMSA"))
aa

al <- clustal(aa)
al

## End(Not run)

Calculate Distances between Sets of Sequences

Description

Implements different methods to calculate distance between sets of sequences based on k-mer distribution, edit distance/alignment or evolutionary distance.

Usage

# k-mer-based methods
distFFP(x, k=3, method="JSD", normalize=TRUE)
distCV(x, k=3)
distNSV(x, k=3, method="Manhattan", normalize=FALSE)
distKMer(x, k=3)
distSimRank(x, k=7)

# edit distance/alignment
distEdit(x)
distAlignment(x, substitutionMatrix=NULL, ...)

# evolutionary distance
distApe(x, model="K80" ,...)

Arguments

x

an object of class XStringSet containing the sequences. For distApe, x needs to be a multiple sequence alignment.

k

size of used k-mers.

method

metric used to calculate the dissimilarity between two k-mer frequency distributions.

substitutionMatrix

matrix with substitution scores (defaults to a matrix with match=1, mismatch=0)

normalize

normalize the k-mer frequencies by the total number of k-mers in the sequence.

model

evolutionary model used.

...

further arguments passed on.

Details

  • Feature frequency profile (distFFP): A FFP is the normalized (by the number of k-mers in the sequence) count of each possible k-mer in a sequence. The distance is defined as the Jensen-Shannon divergence (JSD) between FFPs (Sims and Kim, 2011).

  • Composition Vector (distCV): A CV is a vector with the frequencies of each k-mer in the sequency minus the expected frequency of random background of neutral mutations obtained from a Markov Model. The cosine distance is used between CVs. (Qi et al, 2007).

  • Numerical Summarization Vector (distNSV): An NSV is frequency distribution of all possible k-mers in a sequence. The Manhattan distance is used between NSVs (Nagar and Hahsler, 2013).

  • Distance between sets of k-mers (distkMer): Each sequence is represented as a set of k-mers. The Jaccard (binary) distance is used between sets (number of unique shared k-mers over the total number of unique k-mers in both sequences).

  • Distance based on SimRank (distSimRank): 1-simRank (see simRank).

  • Edit (Levenshtein) Distance (distEdit): Edit distance between sequences.

  • Distance based on alignment score (distAlignment): see stringDist in Biostrings.

  • Evolutionary distances (distApe): see dist.dna in ape.

Value

A dist object.

Author(s)

Michael Hahsler

References

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.

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.

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.

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

Examples

s <- mutations(random_sequences(100), 100)
s

### calculate NSV distance
dNSV <- distNSV(s)

### relationship with edit distance
dEdit <- distEdit(s)

df <- data.frame(dNSV=as.vector(dNSV), dEdit=as.vector(dEdit))
plot(sapply(df, jitter), cex=.1)
### add lower bound (2*k, for Manhattan distance)
abline(0,1/(2*3), col="red", lwd=2)
### add regression line
abline(lm(dEdit~dNSV, data=df), col="blue", lwd=2)

### check correlation
cor(dNSV,dEdit)

Multiple Sequence Alignment (Kalign)

Description

Runs Kalign progressive multiple sequence alignment on a set of sequences.

Usage

kalign(x, param=NULL)
kalign_help()

Arguments

x

an object of class DNAStringSet with the sequences to be aligned.

param

character string with the command line parameters for kalign (see output of kalign_help()).

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

An object of class DNAMultipleAlignment (see BioStrings).

Author(s)

Michael Hahsler

References

Lassmann T., Sonnhammer E. Kalign - an accurate and fast multiple sequence alignment algorithm, BMC Bioinformatics 2005, 6:298

Examples

## Not run: 
dna <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
dna

### align the sequences
al <- kalign(dna)
al

## End(Not run)

Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences

Description

Executes mafft on a set of sequences to obtain a multiple sequence alignment.

Usage

mafft(x, param="--auto")
mafft_help()

Arguments

x

an object of class XStringSet (e.g., DNAStringSet) with the sequences to be aligned.

param

character string with the command line parameters (see output of mafft_help()).

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

An object of class DNAMultipleAlignment (see BioStrings).

Author(s)

Michael Hahsler

References

Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Examples

## Not run: 
### DNA
dna <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
dna

al <- mafft(dna)
al

### inspect alignment
detail(al)

### plot a sequence logo for the first 20 positions
plot(al, 1, 20)

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

al <- mafft(rna)
al

### Proteins
aa <- readAAStringSet(system.file("examples/Protein_example.fasta",
	package="rMSA"))
aa

al <- mafft(aa)
al

## End(Not run)

Run Multiple Sequence Alignment (MUSCLE) on a Set of Sequences

Description

Executes MUSLCE on a set of sequences to obtain a multiple sequence alignment.

Usage

muscle(x, param="")
muscle_help()

Arguments

x

an object of class XStringSet (e.g., DNAStringSet) with the sequences to be aligned.

param

character string with the command line parameters (see output of musce_help()).

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

An object of class DNAMultipleAlignment (see BioStrings).

Author(s)

Michael Hahsler

References

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res. 32(5):1792-1797

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, (5) 113

Examples

## Not run: 
### DNA
dna <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
dna

al <- muscle(dna)
al

### inspect alignment
detail(al)

### plot a sequence logo for the first 20 positions
plot(al, 1, 20)

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

al <- MUSCLE(rna)
al

### Proteins
aa <- readAAStringSet(system.file("examples/Protein_example.fasta",
	package="rMSA"))
aa

al <- MUSCLE(aa)
al

## End(Not run)

Creates Random Mutations of a Sequence

Description

Creates a set of sequences which are random mutations (with base changes, insertions and deletions) for a given DNA, RNA or AA sequence.

Usage

mutations(x, number=1, change=0.01, insertion=0.01, deletion=0.01, prob=NULL)

Arguments

x

A XString or an XStringSet of length 1.

number

number of sequences to create.

change, insertion, deletion

probability of this operation.

prob

a named vector with letter probabilities. 4 for DNA and RNA and 20 for AA (see DNA_BASES, RNA_BASES and the first 20 letters in AA_ALPHABET). The default is to estimate the probabilities from the sequence in x.

Value

A XStringSet.

Author(s)

Michael Hahsler

Examples

### create random sequences
s <- random_sequences(100, number=1)
s

### create 10 sequences with 1 percent base changes, insertions and deletions
m <- mutations(s, 10, change=0.01, insertion=0.01, deletion=0.01)
m

### calculate edit distance between the original sequence and the mutated
### sequences
stringDist(c(s,m))

### multiple sequence alignment
## Not run: 
al <- clustal(c(s,m))
detail(al)

## End(Not run)

Plot Genetic Sequences and Alignments

Description

Plots genetic sequences (RNA/DNA) using sequence logos.

Details

plot creates a sequence logo. Parameters are start (position to start the logo), end (position to end the logo), ic.scale (if TRUE then each column are scaled proportional to its information content).

See Also

seqLogo in seqLogo.


Create a Set of Random Sequences

Description

Creates a set of random DNA, RNA or AA sequences.

Usage

random_sequences(len, number=1, prob=NULL, type=c("DNA", "RNA", "AA"))

Arguments

len

sequence length

number

number of sequences in the set

prob

a named vector with letter probabilities or a transition probability matrix (as produced by oligonucleotideTransitions). 4 letters for DNA and RNA and 20 for AA (see DNA_BASES, RNA_BASES and the first 20 letters in AA_ALPHABET).

type

sequence type

Value

A XStringSet.

Author(s)

Michael Hahsler

Examples

### create random sequences (using given letter frequencies)
seqs <- random_sequences(100, number=10, prob=c(a=.5, c=.3, g=.1, t=.1))
seqs

### check letter frequencies
summary(oligonucleotideFrequency(seqs, width=1, as.prob=TRUE))

### creating random sequences using a random dinocleodite transition matrix
prob <-  matrix(runif(16), nrow=4, ncol=4, dimnames=list(DNA_BASES, DNA_BASES))
prob <- prob/rowSums(prob)

seqs <- random_sequences(100, number=10, prob=prob)
seqs

### check dinocleodite transition probabilities
prob
oligonucleotideTransitions(seqs, as.prob=TRUE)

Compute the SimRank Similarity between Sets of Sequences

Description

Computes the SimRank similarity (number of shared unique k-mers over the smallest number of unique k-mers.)

Usage

simRank(x, k = 7)

Arguments

x

an object of class DNAStringSet containing the sequences.

k

size of used k-mers.

Details

distSimRank() returns 1-simRank().

Value

simRank() returns a similarity object of class "simil" (see proxy). distSimRank() returns a dist object.

Author(s)

Michael Hahsler

References

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

Examples

### load sequences
sequences <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
sequences

### compute similarity
simil <- simRank(sequences)

### use hierarchical clustering
hc <- hclust(distSimRank(sequences))
plot(hc)

Convenience Functions to Convert Strings to Character Vectors

Description

These convenience function can be used to convert character strings into vectors of single characters and back.

Usage

c2s(x)
s2c(x)

Arguments

x

for c2s a single character string and for s2c a vector of single characters.

Value

Either a single character string or a vector of single characters.

Author(s)

Michael Hahsler

Examples

s <- sample(c("A", "C", "G", "T"), 10, replace = TRUE)
s

s2 <- c2s(s)
s2

s2c(s2)