FASTA file format

Crux searches protein sequence databases given in FASTA format. The format is very simple. Every entry consists of a sequence identifier (ID), an optional comment (COMMENT), and a sequence (SEQUENCE). The format looks like this:

  >ID COMMENT
  SEQUENCE

The special character ">" marks the beginning of a new sequence. The ">" character is followed immediately by the sequence identifier. The rest of that line is occupied by the optional comment. Subsequent lines contain the sequence itself.

Some rules about representing sequences:

• A single protein sequence can span multiple lines. The > character occurring at the beginning of the line indicates the end of the sequence.
• Case doesn't matter. Crux Suite converts everything to uppercase.
• White space (spaces and newlines) within the sequence are ignored.
• Characters should be from the amino acid alphabet, which contains twenty characters for amino acids ("ACDEFGHIKLMNPQRSTVWY") and is augmented by four more ambiguous characters ("BUXZ"):

    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  any
    G  glycine                         V  valine
    H  histidine                       W  tryptophan
    I  isoleucine                      Y  tyrosine
    K  lysine                          Z  glutamate or glutamine
    L  leucine                         X  any
    M  methionine                      
    N  asparagine

Here is an example of three sequences in FASTA format.

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