Page tree

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 CodeMeaningMnemonic
AAAdenine
CCCytosine
GGGuanine
UUUracil (only in RNA)
TUTimin (only in DNA)
RA or GpuRine
YC, T or UpYrimidines
KG, T or Ubases which are Ketones
MA or Cbases with aMino groups
SC or GStrong interaction
WA, T or UWeak interaction
Bnot A (i.e. C, G, T or U)B comes after A
Dnot C (i.e. A, G, T or U)D comes after C
Hnot G (i.e., A, C, T or U)H comes after G
Vneither T nor U (i.e. A, C or G)V comes after U
NA C G T UaNy
Xmasked 
-gap of indeterminate length 

Ambigous nucleosides are represented with a labeled pseudoatom.

Code: fasta:dna, fasta:rna

Peptide

Code Aminoacid
AAlanine
BAspartic acid or Asparagine
(represented with an atom list in side-chain)
CCysteine
DAspartic acid
EGlutamic acid
FPhenylalanine
GGlycine
HHistidine
IIsoleucine
KLysine
LLeucine
MMethionine
NAsparagine
OPyrrolysine
PProline
QGlutamine
RArginine
SSerine
TThreonine
USelenocysteine
VValine
WTryptophan
YTyrosine
ZGlutamic acid or Glutamine
(represented with an atom list in side-chain)
Xany
(represented with an X pseudo atom at the α-Carbon atom side chain)
*translation stop
(ignored)
-gap of indeterminate length
(ignored)

Code: fasta:peptide


Export

Not supported yet.

Reference