import.fasta {bios2mds}R Documentation

Reads a file in FASTA format


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


import.fasta(file, = TRUE, = TRUE)



a string of characters to indicate the name of the MSA file to be read.

a logical value indicating whether amino acids should be converted to upper case (TRUE) or not (FALSE). Default is TRUE.

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.


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:

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


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


For further information about FASTA format, see:


Julien Pele


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).


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

[Package bios2mds version 1.2.3 Index]