Mathematica Import/Export Format

FASTA (.fasta, .fa, .fsa, .mpfa)

MIME type: chemical/seq-aa-fasta, chemical/seq-na-fasta
FASTA molecular biology format.
Standard format for storing and exchanging DNA and protein sequences.
Plain text format.
Stores nucleic acid or protein sequences as character strings.
Various conventions are in use to represent meta-information.
Developed in 1988 by William Pearson and David Lipman as part of the FASTA sequence-alignment software.

Import and Export support all common variants of the FASTA file format.

IMPORT AND EXPORT

Import["file.fasta"] imports DNA or protein sequences from a FASTA file.

Export["file.fasta", expr] exports a sequence or a list of sequences to the FASTA format.

Import["file.fasta"] returns a list of strings representing the sequences stored in the file.

Export["file.fasta", str] exports a character string representing a DNA sequence to FASTA.

Export["file.fasta", {str₁, str₂, ...}] exports multiple DNA sequences.

Import["file.fasta", elem] imports the specified element from a FASTA file.

Import["file.fasta", {elem, sub_a, sub_b, ...}] imports a subelement.

Import["file.fasta", {{elem₁, elem₂, ...}}] imports multiple elements.

The import format can be specified with Import["file", "FASTA"] or Import["file", {"FASTA", elem, ...}].

Export["file.fasta", expr, elem] creates a FASTA file by treating expr as specifying element elem.

Export["file.fasta", {expr₁, expr₂, ...}, {{elem₁, elem₂, ...}}] treats each expr_i as specifying the corresponding elem_i.

Export["file.fasta", expr, opt₁->val₁, ...] exports expr with the specified option elements taken to have the specified values.

Export["file.fasta", {elem₁->expr₁, elem₂->expr₂, ...}, "Rules"] uses rules to specify the elements to be exported.

See the reference pages for full general information on Import and Export.

ImportString and ExportString support the FASTA format.

ELEMENTS

General Import elements:

	"Elements"	list of elements and options available in this file
	"Rules"	full list of rules for each element and option
	"Options"	list of rules for options, properties, and settings

Data representation elements:

	"Header"	raw header lines
	"Sequence"	DNA or protein sequences as a list of strings
	"Plaintext"	sequences as formatted text

Import uses the "Sequence" element by default for the FASTA format.

Additional data elements:

	"Data"	"Header" and "Sequence" elements combined in a list
	"LabeledData"	list of rules for each sequence stored in the file

Header line meta-information:

	"Accession"	NCBI accession number for each sequence
	"Description"	locus description text for each sequence
	"GenBankID"	GenBank database identifier
	"Length"	list of integers, representing the length of each sequence

Mathematica uses the standard IUB/IUPAC abbreviations for nucleic acids:

	A	adenosine
	C	cytidine
	G	guanine
	T	thymidine
	U	uracil
	R	purine (G or A)
	Y	pyrimidine (T or C)
	K	ketone (G or T)
	M	amino group (A or C)
	S	strong interaction (G or C)
	W	weak interaction (A or T)
	B	C or G or T
	D	A or G or T
	H	A or C or T
	V	A or C or G
	N	any nucleic acid (A or C or G or T)
	-	gap of indeterminate length

Codes representing amino acids:

	A	alanine (Ala)
	B	either aspartic acid or asparagine
	C	cysteine (Cys)
	D	aspartic acid (Asp)
	E	glutamic acid (Glu)
	F	phenylalanine (Phe)
	G	glycine (Gly)
	H	histidine (His)
	I	isoleucine (Ile)
	K	lysine (Lys)
	L	leucine (Leu)
	M	methionine (Met)
	N	asparagine (Asn)
	P	proline (Pro)
	Q	glutamine (Gln)
	R	arginine (Arg)
	S	serine (Ser)
	T	threonine (Thr)
	U	selenocysteine
	V	valine (Val)
	W	tryptophan (Trp)
	Y	tyrosine (Tyr)
	Z	either glutamic acid or glutamine
	X	any amino acid
	*	translation stop
	-	gap of indeterminate length

OPTIONS

Import option:

"HeaderFormat"

Automatic

specifies the format of the header

Import uses a large built-in library of header format specifications found in common variants of the FASTA format.

By setting "HeaderFormat" to a list of literal strings and names of meta-information elements, any header line format can be specified on Import.

"HeaderFormat"->{"gi|", "DatabaseIndex", "|gb|", "Accession", "|", "Description"} is a setting typical for NCBI Fasta files.

Advanced Export option:

"LineWidth"

maximum number of characters in a line