FASTA file format
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.
Code: fasta
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
Peptide
Code |
Aminoacid |
A |
Alanine |
B |
Aspartic acid or Asparagine |
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 |
X |
any |
* |
translation stop |
- |
gap of indeterminate length |
Code: fasta:peptide