PlantsP - FASTA Sequence Format

PlantsP-Functional Genomics of Plant Phosphorylation

FASTA Sequence Format

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data.

The description line starts with a greater than symbol (">").
The word following the greater than symbol (">") immediately is the "ID" (name) of the sequence, the rest of the line is the description.
The "ID" and the description are optional.
All lines of text should be shorter than 80 characters.
The sequence ends if there is another greater than symbol (">") symbol at the beginning of a line and another sequence begins.

The following example contains two sequences (Example1, Example2):

>Example1 envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL LAAVEAQQQMLKLTIWGVK >Example2 synthetic peptide HITREPLKHIPKERYRGTNDTLSPQIESIWAAELDRYKLVKTNCSNVS

Sequences should be in single letter standard IUB/IUPAC amino acid and nucleic acid codes. There is some variablitity among programs in support for the following:

Lower case letters are generally acceptable, but in some programs have special meanings.
Gaps introduced by alignment programs are frequently represented by the hyphen or period characters.
The end of a sequence is sometimess represented by a asterisk (*). Less frequently, sequences for which the reported region begins or ends within the known sequence may begin or end wit a slash (/).
Unknown bases are generally represented by N, and sometimes by X.
Unknown amino acid residues are represented by X, and the ambiguous acid/amide residues by B (D or N) and Z (E or Q). Selenomethionine is sometimes represented as "O", and seleocysteine as "U", but many programs will treat these as an errors.

The accepted nucleic acid codes 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) X --> A G C T (any)

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 tryptophane I isoleucine Y tyrosine K lysine Z glutamate or glutamine L leucine X any M methionine * translation stop N asparagine O selenomethionine