Genetics Program
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Technical Corner
This page contains technical details of laboratory protocols and genetic analyses that have been used or developed in the Genetics Program. Members of the Genetics Program have had great success using these protocols but make no guarentees of your success.
Cloning of Microsatellite-Enriched Genomic Libraries:
We recently discovered that the SAU linkers described in these protocols are highly self complimentary. This means that the PCR steps in the protocol will work very poorly. Although the general enrichment strategy in the protocols is correct, the linkers are extremely inefficient. We have devoted much work to solving this and other problems. A revised protocol will be posted here in the near future.
These files contain the detailed, lab bench tested version of a microsatellite cloning technique developed over several years in the Genetics Program. We have had success with this technique and hope you find it useful as well. The text files are not recommended because all formatting is lost. There are two versions of the protocol that use different means to accomplish subtractive hybridization, one using nylon membrane and the other using streptavidin-coated metal "beads". They both have advantages and disadvantages but most people think the bead method is better and easier despite the higher cost. You be the judge.
Microsatellite Cloning Protocol - Bead version: [PDF]
Microsatellite Cloning Protocol - Nylon version: [PDF]
Microsatellite Workshop Spring 2000:
In March 2000, Stacey Lance, Robert Fleischer and I ran a microsatellite development workshop at the NMNH's Genetics Program. This workshop was supported by the University of Maryland-Smithsonian Research Training Grant in Small Population Biology from NSF. We had 10 students come to the lab for ten days to develop microsatellites in their species of interest [download PDF].
CIProgPPC 1.01b:
Downloads contain a PowerPC version of CIProgram 1.01b, a ReadMe file and a sample data set. This program was based on Steel et al. 1996 and calculates average uncorrected inter-clade distances, standard deviation, and upper & lower 95% confidence intervals (Jukes-Cantor correction). Steel et al. found this to be an excellent method of obtaining tighter confidence intervals for calculating molecular clock parameters: time, molecular rate, and level of divergence between clades. For more information on method of analysis see Steel reference below.
Steel, M., Cooper, A., Penny, D. 1996. Confidence intervals for the divergence time of two clades. Syst. Biol. 45(2):127-134.CIProgramPPC.sea.hqx (80k)
CIProgramPPC.sit.hqx (60k)
One file is a self-extracting archive (.sea) and the other is compressed using StuffIt. Both are BinHexed (.hqx) for Macintosh.Revision: February 2003
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