Background

Background — Formats and Nomenclature

BPSEQ

The standard BPSEQ format is a three-column tab-separated text file:

Index   Nucleotide   PairingPartner
1       G            29
2       G            28
3       G            27
...

• Index is 1-based.
• PairingPartner is 0 for unpaired positions, or the 1-based index of the paired nucleotide.

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Extended BPSEQ

RNA2DUnifier introduces an extended BPSEQ format that adds one column for each of the 12 Leontis–Westhof interaction families. Each extra column lists the 1-based index (or indices) of pairing partners for that specific interaction type at that position. 0 means no partner of that type.

Example header:

Index   Nucleotide   cWW   tWW   cWH   tWH   cWS   tWS   cHH   tHH   cHS   tHS   cSS   tSS

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Leontis–Westhof Nomenclature

The 12 geometric families describe base pairs in terms of the interacting edges (Watson–Crick W, Hoogsteen H, Sugar S) and the glycosidic bond orientation (cis c / trans t):

Code	Edges	Orientation
cWW	W / W	cis
tWW	W / W	trans
cWH	W / H	cis
tWH	W / H	trans
cWS	W / S	cis
tWS	W / S	trans
cHH	H / H	cis
tHH	H / H	trans
cHS	H / S	cis
tHS	H / S	trans
cSS	S / S	cis
tSS	S / S	trans

Canonical Watson–Crick base pairs (A–U, G–C) are classified as cWW. The tWW type is also considered canonical by the library.

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