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.

Name

*.fasta

Application purpose

Sequence information generated by the FASTA sequence alignment package.

Format

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").

Example

>foobar A:1-6
gX[5MC]ggau

>foobar B:1-6
auccX[7MG]c

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

2'OMe

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

2'F

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

Fasta File