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The restriction enzymes selected usually have rare or few restriction sites on bacterial chromosomal DNA, resulting in larger fragments, which can only be separated by PFGE methodology.
In the case of some genome projects, multiple optical-maps can be useful as they can provide complementary information and help place contigs that have few restriction sites.
Unique placement is, however, not possible for sequences contained in repeats, and for sequences containing few restriction sites especially if the sizes of the restriction fragments occur commonly in the optical map.
Although rice centromeres are analyzable by optical mapping, mammalian centromeres, being larger and more complex, may challenge our ability to span regions bearing few restriction sites with ~500 kb molecules.
In the whole mtDNA study, much larger sample sizes were employed to increase the sensitivity of the mtDNA assay, but only two restriction enzymes were used and consequently, only a few restriction sites were analyzed.
Alignments show that these new maps are essentially identical to BtOM1.0 except for a few restriction site differences (2 extra cuts, 5 missing cuts for chromosome 27; 4 missing cuts for chromosome 28).
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