IML format

Intron model files describe the format of splice site combinations that are considered as potential intron. Discriminatory attributes of biological introns are (1st) the distance of the donor/acceptor pair, (2nd) the combination of their splice site sequences. Each model block is introduced by a header line.

#MODEL minDist maxDist

where #MODEL introduces a new model, and minDist respectively maxDist delimit the boundaries on the lengths of valid introns that are described by the model. Subsequently, a list of donor/acceptor sequences that may co-occur in valid introns is provided.

donorSeq1 acceptorSeq1
donorSeq2 acceptorSeq2
$\ldots$ $\ldots$

The sequences are the strings directly adjacent to exons, and may be redundant — as combinations are evaluated — as their length may vary, even amongst donors and acceptors.

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