Supported formats

Supported Formats

Formats are represented by the RNAFormat enum. The library detects the format from file content, not from the file extension.

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AAS — Arc Annotated Sequence

Weak bonds expressed as a semicolon-separated list of index pairs. The nucleotide sequence is optional and precedes the bond list. Indices are 1-based.

ACGUACGU
(1,8);(2,7);(3,6)

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AAS NO SEQUENCE

Identical to AAS but without the nucleotide sequence:

(1,8);(2,7);(3,6)

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BPSEQ

Three-column format: position index, nucleotide, bonding partner (0 if unpaired).

1 A 8
2 C 7
3 G 6
4 U 0
5 A 0
6 C 3
7 G 2
8 U 1

Optionally supports four header lines starting with Filename, Organism, Accession, Citation.

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CT — Connect Format

Six-column format. The header line must contain one of the keywords ENERGY, Energy, or dG.

8 ENERGY = -3.5
1 A 0 2 8 1
2 C 1 3 7 2
3 G 2 4 6 3
4 U 3 5 0 4
5 A 4 6 0 5
6 C 5 7 3 6
7 G 6 8 2 7
8 U 7 1 1 8

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DB — Dot-Bracket Notation

The nucleotide sequence (optional) precedes the structure string. . denotes unpaired bases; matching bracket pairs denote bonds. Supports extended notation for pseudoknots.

ACGUACGU
(((...)))

Extended pseudoknot notation:

ACGUACGUACGU
((((AAAA))))aaaa

Supported bracket symbols: (), [], {}, <>, and matching uppercase/lowercase letter pairs.

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DB NO SEQUENCE

Like DB but without the nucleotide sequence:

(((...)))

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FASTA

Standard bioinformatics format. Contains only the nucleotide sequence — no structural information.

>sequence_name
ACGUACGUACGU

⚠️ FASTA cannot be translated into any structural format, as it carries no bond information.

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Format Comparison

Format	Has Sequence	Has Structure	Pseudoknots
AAS	Optional	✅	✅
AAS NO SEQUENCE	❌	✅	✅
BPSEQ	✅	✅	✅
CT	✅	✅	✅
DB	Optional	✅	✅
DB NO SEQUENCE	❌	✅	✅
FASTA	✅	❌	—

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See Also

• Format Translation — conversion matrix and API
• Home