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Because most pointer sequences are too short to guide accurate IES removal and unscrambling of an entire gene, in part because of redundancy [15], other factors must assist unscrambling.
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Conventional IESs are always bound by pairs of direct repeats, or pointer sequences, which are thought to guide proper assembly of macronuclear-destined segments [ 1].
Hence by the onset of more complex events like inversion of segments 2 and 1 or segment 9 translocation in S. lemnae actin I, the precursor molecule has already been shortened by 280 bp, the combined lengths of IES 1 5 and 8 plus one copy of each of the flanking pointer sequences that has been consumed.
Pointer sequences containing the word AGT are never frame-preserving.
The CNE model for gene scrambling [ 7] is based on a side-effect of the postulated mechanism for removing IESs using flanking "key" or "pointer" sequences, similar to the repeats generated by various types of transposons.
Only one copy of each sequence is stored in memory, while the hash tables store pointers to all duplicates.
The pointer sequences automatically restore the correct ordering of fragments during developmental processing of IESs.
Sequence is different.
JT: Sequence is essential.
Sequencing is out.
A Pointer Update Unit and a Pointer Buffer are combined to remove the overhead resulted from pointer-calculations and stack pushes during the parallel depth-first-traversal process.
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