FASTA format description

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is:

>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK

IUPAC-IUB Codes

Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino acid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).
The nucleic acid codes supported are:

     A --> adenosine           M --> A C (amino)
     C --> cytidine            S --> G C (strong)
     G --> guanine             W --> A T (weak)
     T --> thymidine           B --> G T C
     U --> uridine             D --> G A T
     R --> G A (purine)        H --> A C T
     Y --> T C (pyrimidine)    V --> G C A
     K --> G T (keto)          N --> A G C T (any)
                               - --> gap of indeterminate length

For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:

 A  alanine                      P  proline
 B  aspartate or asparagine      Q  glutamine
 C  cystine                      R  arginine
 D  aspartate                    S  serine
 E  glutamate                    T  threonine
 F  phenylalanine                U  selenocysteine
 G  glycine                      V  valine
 H  histidine                    W  tryptophan
 I  isoleucine                   Y  tyrosine
 K  lysine                       Z  glutamate or glutamine
 L  leucine                      X  any
 M  methionine                   *  translation stop
 N  asparagine                   -  gap of indeterminate length

IUPAC-IUB/GCG Ambiguity Codes

the ambiguity codes used in DNA sequences
which of the four bases (A,C,T,G) are represented by the codes
the complement of the ambiguity code

Codes	Meaning	Complement
A	A (adenine)	T
C	C (cytosine)	G
G	G (guanine)	C
T/U	T (thymine in DNA; uracil in RNA)	A
M	A or C	K
R	A or G	Y
W	A or T	W
S	C or G	S
Y	C or T	R
K	G or T	M
V	A or C or G	B
H	A or C or T	D
D	A or G or T	H
B	C or G or T	V
X/N	G or A or T or C	X
.	not G or A or T or C	.

Reference:

Authority:  Nomenclature Committee of the International Union of Biochemistry 
Reference:  Cornish-Bowden, A.  Nucl Acid Res 13, 3021-3030 (1985)
IUPAC/IUB:  International Union of Pure and Applied Chemistry/International Union of Biochemistry

November 23, 2008 (Sunday)