import.fasta: Reads a file in FASTA format

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Reads a file in FASTA format

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

The import.fasta function was developed for the bios2mds R package (Julien PELE [aut], Jean-Michel BECU [aut], Marie CHABBERT [cre]). .

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.

Examples

  # Importing MSA file in FASTA format
  aln <- import.fasta(system.file("msa/toy2_align.fa", package = "Bios2cor"))

Bios2cor documentation built on April 4, 2025, 4:14 a.m.