Physical Mapping Calculators - Random Probes

This calculator could help you to predict the progress of physical mapping projects based on hybridisations with short "anchor" probes, chosen randomly. You can calculate expected values of several measures of the experimental progress.

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What are these measures?

A contig is a group of one or more clones linked together by anchors they share; a contig formed by only one anchor is called a singleton. Clones on the ends of adjacent contigs, however, can actually overlap but may not have any anchors in common, thus resulting in breaks in contigs. This case is referred to as an undetected overlap between the respective pair of contigs. A gap is a segment of the genome with no contigs on it.

These predictions are based on the following assumptions:

All library clones are selected randomly from the genome
All probes are selected randomly from the genome
Clones and probes are independently distributed
All inserts are of the same size
Such experimental factors as chimerism, repeats and false positive/negative results are ignored, so expect your project to progress slower than the ideal model :-(


The predictions are based on the mathematical results published in the following papers:

Arratia, R., Lander, E. S., Tavare, S., and Waterman, M. S. (1991) Genomic mapping by anchoring random clones: a mathematical analysis. Genomics 11, 806-827.

Barillot, E., Dausset, J., and Cohen, D. (1991) Theoretical analysis of a physical mapping strategy using random single-copy landmarks. Proc. Nat. Acad. Sci. USA 88, 3917-3921.

Ewens, W. J., Bell, C. J., Donelly, P. J., Dunn, P., Matallana, E., and Ecker, J. R. (1991) Genome mapping with anchored clones: theoretical aspects. Genomics 11, 799-805.

Grigoriev, A. V. (1993) Theoretical predictions and experimental observations of genomic mapping by anchoring random clones. Genomics, 15, 311-316.

Comments are most welcome - just click on my name below to email me

Copyright 1996 Andrei Grigoriev

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