FASTA file format¶
Code : fasta
Import¶
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. See also
FASTA import options
Code : fasta:dna, fasta:rna
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.
Peptide¶
Code : ** fasta:peptide**
| 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) |
Export¶
Not supported yet.