FASTA file format


    Marvin import the FASTA files if the comment line of it starts with a '>' character. If the sequence type is not specified, Marvin will try to guess it from the comment header and from the sequence.

    Code : fasta See also FASTA import options

    DNA, RNA

    We import the following codes.

    Nucleic Acid Code Meaning Mnemonic
    A A Adenine
    C C Cytosine
    G G Guanine
    U U Uracil (only in RNA)
    T U Timin (only in DNA)
    R A or G puRine
    Y C, T or U pYrimidines
    K G, T or U bases which are Ketones
    M A or C bases with aMino groups
    S C or G Strong interaction
    W A, T or U Weak interaction
    B not A (i.e. C, G, T or U) B comes after A
    D not C (i.e. A, G, T or U) D comes after C
    H not G (i.e., A, C, T or U) H comes after G
    V neither T nor U (i.e. A, C or G) V comes after U
    N A C G T U aNy
    X masked
    - gap of indeterminate length

    Ambigous nucleosides are represented with a labeled pseudoatom.

    Code : fasta:dna, fasta:rna


    Code Aminoacid
    A Alanine
    B Aspartic acid or Asparagine (represented with an atom list in side-chain)
    C Cysteine
    D Aspartic acid
    E Glutamic acid
    F Phenylalanine
    G Glycine
    H Histidine
    I Isoleucine
    K Lysine
    L Leucine
    M Methionine
    N Asparagine
    O Pyrrolysine
    P Proline
    Q Glutamine
    R Arginine
    S Serine
    T Threonine
    U Selenocysteine
    V Valine
    W Tryptophan
    Y Tyrosine
    Z Glutamic acid or Glutamine (represented with an atom list in side-chain)
    X any (represented with an X pseudo atom at the α-Carbon atom side chain)
    * translation stop (ignored)
    - gap of indeterminate length (ignored)

    Code : fasta:peptide


    Not supported yet.