import.fasta: Reads a file in FASTA format

In bios2mds: From Biological Sequences to Multidimensional Scaling

Description

Reads a Multiple Sequence Alignment (MSA) file in FASTA format (.fasta or .fa extension).

Usage

import.fasta(file, aa.to.upper = TRUE, gap.to.dash = TRUE)

Arguments

file	a string of characters to indicate the name of the MSA file to be read.
aa.to.upper	a logical value indicating whether amino acids should be converted to upper case (TRUE) or not (FALSE). Default is TRUE.
gap.to.dash	a logical value indicating whether the dot (.) and tilde (\sim) gap symbols should be converted to dash (-) character (TRUE) or not (FALSE). Default is TRUE.

Details

Initially, FASTA (for FAST-ALL) was the input format of the FASTA program, used for protein comparison and searching in databases. Presently, FASTA format is a standard format for biological sequences.

The FASTA formatted file of a single sequence displays:

• a single-line description beginning with a greater-than (>) symbol. The following word is the identifier.

• followed by any number of lines, representing biological sequence.

For multiple alignments, the FASTA formatted sequences are concatenated to create a multiple FASTA format.

Value

A object of class 'align', which is a named list whose elements correspond to sequences, in the form of character vectors.

Note

For further information about FASTA format, see: http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

Author(s)

Julien Pele

References

Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 27:2444-2448.

See Also

read.fasta function from bio3d package.
read.fasta function from seqinr package.
read.FASTA function from aaMI package (archived).

Examples

# reading of the multiple sequence alignment of human GPCRS in FASTA format:
aln <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))

Example output

Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

bios2mds documentation built on April 14, 2020, 5:08 p.m.