Output formats

Output Formats

Extended BPSEQ

The extended BPSEQ is a tab-separated file with one row per nucleotide position and one column per Leontis–Westhof interaction family:

Index	Nucleotide	cWW	tWW	cWH	tWH	cWS	tWS	cHH	tHH	cHS	tHS	cSS	tSS
1	G	29	0	0	0	0	0	0	0	0	0	0	0
2	G	28	0	0	0	0	0	0	0	0	0	0	0
5	U	25	0	0	0	0	0	0	0	0	35	0	0
...

• Every nucleotide in the sequence appears (one row per position).
• 0 means no partner of that type.
• Multiple partners for a single type at one position are listed as comma-separated values (e.g., 3,17). To produce extended BPSEQ, pass true as the extended argument:

String result = unifier.process(inputFile, ToolType.FR3D, true);

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Canonical BPSEQ

The canonical BPSEQ follows the classic three-column format and contains only positions that participate in at least one canonical pair (cWW or tWW):

1	G	29
2	G	28
4	C	26
...

To produce canonical BPSEQ, pass false as the extended argument:

String result = unifier.process(inputFile, ToolType.FR3D, false);

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