Sequence data contains sequences of residues without structural data. The derivation and accuracy of such files is the subject of research but the formats tend to be simple.



Application purpose

Sequence information generated by the FASTA sequence alignment package.


Every Rosetta RNA fasta file will look a little different from ordinary FASTA files. For one thing, there will be chain information in the header line (the one that begins with a right angle bracket) and there may be multiple chains. For another, the RNA sequence will be all lowercase (to permit specification of uppercase protein residues and lowercase RNA). For a third, chemically modified nucleotides may be specified by replacing an ordinary letter like u with a special code X which is then modified by a "full residue name" like X[5MU] (which translates to "5-methyl uridine").


>foobar A:1-6

>foobar B:1-6

This format is used by applications including stepwise, ERRASER2, and FARFAR2.

An incomplete list of supported chemically modified nucleotides

ICY - isocytidine
IGU - isoguanidine
INO - inosine


A2M - 2'-O-methyladenosine
OMC - 2'-O-methylcytidine
OMG - 2'-O-methylguanosine
OMU - 2'-O-methyluridine

Other 2' modifications

5JO - 2'-O-prop-2-yn-1-yladenosine
A44 - 2'-O-methoxyethyladenosine
C43 - 2'-O-methoxyethylcytidine
C5L - 2'-O-methoxyethyl-5-methylcytidine
G48 - 2'-O-methoxyethylguanosine
U36 - 2'-O-methoxyethyluridine


FMA - 2'-fluoroadenosine
FMC - 2'-fluorocytidine
FMG - 2'-fluoroguanosine
FMU - 2'-fluorouridine

OP1 => SP1

SRA - adenosine-thiomonophosphate (enantiomer 1)
SRC - cytidine-thiomonophosphate (enantiomer 1)
SRG - guanosine-thiomonophosphate (enantiomer 1)
SRU - uridine-thiomonophosphate (enantiomer 1)

OP1 => SP2

SSA - adenosine-thiomonophosphate (enantiomer 2)
SSC - cytidine-thiomonophosphate (enantiomer 2)
SSG - guanosine-thiomonophosphate (enantiomer 2)
SSU - uridine-thiomonophosphate (enantiomer 2)

Modified bases

1AP - 2,6-diaminopurine
1MA - 1-methyl-6-hydroadenosine
2MA - 2-methyladenosine
2MG - 2-methylguanosine
2MU - 2'O-,5-dimethyluridine
4OC - 2'O-,5-dimethylcytidine
5MC - 5-methylcytidine
5MU - 5-methyluridine
BRU - 5-bromo-2'O-deoxyuridine
5BU - 5-bromouridine
7MG - 7-methyl-8-hydroguanosine
G7M - 7-methyl-guanosine
7DA - 7-deaza-2'O-deoxyadenosine
M2G - 2-dimethylguanosine
MA6 - 6-dimethyladenosine
PSU - pseudouridine
UR3 - 3-methyluridine
6MZ - 6-methyladenosine
1MG - 1-methylguanosine
4SU - 4-thiouridine
3TD - 3-methylpseudouridine
H2U - dihydrouridine
MIA - 2-methylthio-6-isopentenyladenosine
5FU - 5-fluorouridine
5IU - 5-iodouridine
2AP - 2-aminopurine
PUR - purine
6MG - 6-methylguanosine
5FC - 5-fluorocytidine
8OG - 8-oxo-2'-deoxyguanosine
OMI - 2'O-methylinosine
CFM - 2'O-methyl-5-formylcytidine
PPU - puromycin
AET - N6-methyl,N6-carbamoylthreonyladenosine
T6A - N6-carbamoylthreonyladenosine
3MC - 3-methylcytidine
52C - 2',5-methylcytidine
RIA - 2'-(5'-phospho)ribosyladenosine
QUO - queuesine
YYG - wybutosine
O2W - 2'-methylwybutosine
NMT - 2'-methylcarbamoyl-5-methyluridine
M3G - 2,2,2'-trimethylguanosine

See Also