Optical Mapping

Abstract

Optical mapping generates an ordered restriction map of a DNA molecule, that is, an ordered enumeration of the restriction sites along with the estimated lengths of the restriction fragments between consecutive restriction sites and various statistics, which model the errors in estimating the restriction fragment lengths and due to unrepresented and misrepresented restriction sites in the map. They have applications in improving the accuracy and algorithmic efficiency of sequence assembly, validating assembled sequences, characterizing gaps in the assembly and identifying candidates for finishing steps in a sequencing project, etc.

Keywords: physical mapping; single molecule method; Bayesian inference; map assembly algorithm; map‐assisted sequence assembly and validation

Figure 1.

Key ideas for computing an accurate consensus optical map with a statistical algorithm. The input to the algorithm is a set of imperfect single molecule optical maps of the same genomic region.

Figure 2.

Schematics of shotgun optical mapping approach. (a) Shotgun mapping with large randomly sheared genomic DNA fragments. (b) Random fragmentation of genomic DNA during mechanical manipulation. Surface‐mounted molecules are digested by a restriction enzyme. (c) Automated image acquisition. (d) Map construction using a Bayesian algorithm. (e) Final map is visualized along with all the aligned molecules. (Reproduced from Lai et al., .)

Figure 3.

A consensus optical map computed by Gentig from a large set of imperfect single molecule optical maps. The single molecule maps are generated in silico. The maps are visualized with Genscape.

Figure 4.

An optical map aligned to sequence contigs, also visualized with Genscape. The consensus optical map of a genome is shown on top in red (at two different resolutions). In silico maps generated from the sequence contigs are aligned to the consensus map in order to validate the mutual consistency between the map and the sequence in order to detect sequence assembly errors, sequence contig locations and orientations, and gap between the sequence contigs.

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References

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How to Cite close
Mishra, Bud(Sep 2005) Optical Mapping. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005364]