FASTA Format for Nucleotide Sequences

In FASTA format the line before the nucleotide sequence, called the FASTA definition line, must begin with a carat (">"), followed by a unique SeqID (sequence identifier).

• The SeqID must be unique for each nucleotide sequence and should not contain any spaces. Please limit the SeqID to 25 characters or less. The SeqID can only include letters, digits, hyphens (-), underscores (_), periods (.), colons (:), asterisks (*), and number signs (#). The sequence identifier will be replaced with an Accession number by the database staff when your submission is processed.

  ›SeqABCD

• Information about the source organism from which the sequence was obtained follows the SeqID and must be in the format [modifier=text]. Do not put spaces around the "=". At minimum, the scientific name of the organism should be included. Optional modifiers can be added to provide additional information. A complete list of available source modifiers and their format is available.

  ›SeqABCD [organism=Mus musculus] [strain=C57BL/6]

Note in all cases, the FASTA definition line must not contain any hard returns. All information must be on a single line of text. If you have trouble importing your FASTA sequences, please double check that no returns were added to the FASTA definition line by your editing software.

Examples of properly formatted FASTA definition lines for nucleotide sequences:

›Seq1 [organism=Streptomyces lavendulae] [strain=456A]

›ABCD [organism=Plasmodium falciparum] [isolate=ABCD]

›DNA.new [organism=Homo sapiens] [chromosome=17] [map=17q21] [moltype=mRNA]

The line after the FASTA definition line begins the nucleotide sequence. Unlike the FASTA definition line, the nucleotide sequence itself can contain returns. It is recommended that each line of sequence be no longer than 80 characters. Please only use IUPAC symbols within the nucleotide sequence. For sequences that are not contained within an alignment, do not use "?" or "-" characters. These will be stripped from the sequence. Use the IUPAC approved symbol "N" for ambiguous characters instead.