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

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

FASTA format description

 A sequence in FASTA format consists of:
o One line starting with a ">" sign, followed by a sequence identification
code. 
It is optionally be followed by a textual description of the sequence. Since
it is not part of the official description of the format, software can choose
to ignore this, when it is present.
o One or more lines containing the sequence itself.
 A file in FASTA format may comprise more than one sequence.

 The FASTA format is sometimes also referred to as the "Pearson" format (after the
author of the FASTA program and ditto format).

FASTA format example

Use the mouse to cut-and-paste the sequence(s) below into the appropriate input window.

>BTBSCRYR
tgcaccaaacatgtctaaagctggaaccaaaattactttctttgaagacaaaaactttca
aggccgccactatgacagcgattgcgactgtgcagatttccacatgtacctgagccgctg
caactccatcagagtggaaggaggcacctgggctgtgtatgaaaggcccaattttgctgg
gtacatgtacatcctaccccggggcgagtatcctgagtaccagcactggatgggcctcaa
cgaccgcctcagctcctgcagggctgttcacctgtctagtggaggccagtataagcttca
gatctttgagaaaggggattttaatggtcagatgcatgagaccacggaagactgcccttc
catcatggagcagttccacatgcgggaggtccactcctgtaaggtgctggagggcgcctg
gatcttctatgagctgcccaactaccgaggcaggcagtacctgctggacaagaaggagta
ccggaagcccgtcgactggggtgcagcttccccagctgtccagtctttccgccgcattgt
ggagtgatgatacagatgcggccaaacgctggctggccttgtcatccaaataagcattat
aaataaaacaattggcatgc

>crab_anapl ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-

CRYSTALLIN).
MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMR
SPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDM
VEIH
GKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPR
KQ
SDVPERSIPITREEKPAIAGAQRK

>crab_anapl ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-

CRYSTALLIN).
MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMR
SPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDM
VEIH
GKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPR
KQ
SDVPERSIPITREEKPAIAGAQRK
>crab_bovin ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFPASTSLSPFYL
R
PPSFLRAPSWIDTGLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDV
IEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLAITSSLSSDGVLTVNGP
RK
QASGPERTIPITREEKPAVTAAPKK
>crab_chick ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDITIHNPLVRRPLFSWLTPSRIFDQIFGEHLQESELLPTSPSLSPFLMR
SPFFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDM
IEIH
GKHEERQDEHGFIAREFSRKYRIPADVDPLTITSSLSLDGVLTVSAPR
KQ
SDVPERSIPITREEKPAIAGSQRK
>crab_human ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFPTSTSLSPFYLR
PPSFLRAPSWFDTGLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGD
VIEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVNGP
RK
QVSGPERTIPITREEKPAVTAAPKK
>crab_mesau ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFSTATSLSPFYL
R
PPSFLRAPSWIDTGLSEMRMEKDRFSVNLDVKHFSPEELKVKVLGD
VVEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVNGP
RK
QASGPERTIPITREEKPAVTAAPKK
>crab_mouse ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN) (P23).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFSTATSLSPFYL
R
PPSFLRAPSWIDTGLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDV
IEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLAITSSLSSDGVLTVNGP
RK
QVSGPERTIPITREEKPAVAAAPKK
>crab_rabit ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFPTSTSLSPFYLR
PPSFLRAPSWIDTGLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDV
IEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVNGP
RK
QAPGPERTIPITREEKPAVTAAPKK
>crab_rat ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
MDIAIHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFSTATSLSPFYL
R
PPSFLRAPSWIDTGLSEMRMEKDRFSVNLDVKHFSPEELKVKVLGD
VIEV
HGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVNGP
RK
QASGPERTIPITREEKPAVTAAPKK
>crab_squac ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-
CRYSTALLIN).
MDIAIQHPWLRRPLFPSSIFPSRIFDQNFGEHFDPDLFPSFSSMLSPFY
W
RMGAPMARMPSWAQTGLSELRLDKDKFAIHLDVKHFTPEELRVKIL
GDFI
EVQAQHEERQDEHGYVSREFHRKYKVPAGVDPLVITCSLSADGVLT
ITGP
RKVADVPERSVPISRDEKPAVAGPQQK