Description

This track contains all perfect 'microsatellite' repeats with between 2 and 10 bp repeat units and 10 or more perfect copies. Over 90% of the items will be multi-allelic polymorphisms. Click on an individual repeat element within the track for more information about that item.

Methods

This track was created by using three programs: Tandyman, display_VNTR and Primeleftright.

• Tandyman is a program for identifying perfectly identical tandem repeat sequences written by Robert Leach. It has been shown that the number of continous perfect repeats in a microsatellite is perhaps the primary factor in generating polymorphism at that locus.
• display_VNTR is a wrapper for tandyman which, among other things, creates a fasta delimited file suitable for automated primer design. This is available from Gerome Breen.
• Primeleftright is a simple program which uses a strict set of thermodynamic parameters to select primers giving the smallest possible PCR product. This is available from Leo Schalkwyk.

These programs were used (via linking Perl scripts to reformat output and input files) to find all perfect 'microsatellite' repeats with between 2 and 10 bp repeat units and 10 or more perfect copies.

Particular features include:

The high probability (>90%) that elements of this track are polymorphic and may have multiple alleles.

The exclusion of mono-nucleotide repeats. These are particularly common but very difficult to genotype.

The presence of a "distance to next repeat" score in bp allowing users to filter overlapping repeats.

The primer designs are a first pass design which will improve in future versions of this data. The main problem with the design is the tendency of primers to end up in repeat regions near the repeat of interest. Users may want to carry out their own QC on the quality of the designs and we expect a good proportion of the design to be usable.

Credits

We'd like to thank Gerome Breen and Nik Ammar and the SGDP Centre at the Institute of Psychiatry for providing the data used to generate this track. If you wish to cite this data please cite
Breen et al. "Distributions of Polymorphic Microsatellites in Mammalian and Other Genomes." (in preparation).