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 :-(
References
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.
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Copyright 1996 Andrei Grigoriev
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