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<TITLE> FASTA format description </TITLE>
<!-- Changed by: Sergei Shavirin, 2-Apr-1996 -->
<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >
<h1>FASTA format description</h1>
<HR>
<p>
<dd>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
<BR>format is:
<PRE>
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK
</PRE>
<dd> 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).
<BR>
The nucleic acid codes supported are:
<PRE>
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
</PRE>
For those programs that use amino acid query sequences (BLASTP
and TBLASTN), the accepted amino acid codes are:
<PRE>
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
</PRE>
<HR>
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