Physical Mapping Calculators - Random Fingerprinting
These calculators could help you to predict the progress of physical mapping projects based on fingerprinting a large number of library clones, chosen randomly (eg by restriction analysis or "shotgun" sequencing). You can calculate expected values of several measures of the experimental progress.
Two calculators are shown: one at the top is based on the (classic by now) paper by Lander and Waterman (1988), while that below - on a more recent publication of Roach (1995) and his personal communication. Their results are very similar for low library redundacy but start to differ at redundancies of three and higher, where the model of Jared Roach gives more consistent estimates (eg, for the contig length).
Another difference is in calculation of the expected number of gaps. Roach (1995) calculated the total number of all the gaps in the final map (which is the number of contigs plus one for a linear target), while Lander and Waterman (1988) provided results for "real" gaps (as opposed to undetected overlaps). You may need to enlarge your browser window or open a new window to see both calculators simulataneously.
Lander and Waterman
What are these measures?
A contig is a group of one or more clones overlapping by at least minimum overlap parameter above (given as a percentage of a clone length), so this fact is detected by sufficient similarity of their fingerprints. A contig formed by only clone is called a singleton. A gap is a segment of the genome with no contigs on it.
These predictions are based on the following assumptions:
Such experimental factors as chimerism, repeats and false positive/negative results are ignored, so expect your project to progress slower than the ideal model :-(
- All library clones are selected randomly from the genome
- Minimum overlap between two clones is always detected
- All inserts are of the same size
The predictions are based on the mathematical results published in
Lander, E. and Waterman, M. S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2, 231-239.
Roach, J. C. (1995) Random Subcloning. Genome Research. 5, 464-473.
See also his web page on the subject.
Comments are most welcome - just click on my name below to email me
Copyright 1996 Andrei Grigoriev
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