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.

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.

Reference