Database Searches for Polymorphism and Primer Sequence Information

We offer a direct query interface to our database so that you may obtain polymorphism and sequence information about most markers in this release. For more detailed information about inbred rat strains visit the Jackson Laboratories web site.

Search for markers by position/polymorphism

View polymorphism table for all markers or download the polymorphism table via anonymous ftp. Note: Polymorphism data is calculated only for loci that amplified successfully in any given strain. To view statistics for these calculations you may view the following table--polymorphism information with marker numbers. Warning--This is a very large table! In each square the number to the left represents the percent polymorphism, the top number on the right is the number of monomorphic markers, the middle is the number of polymorphic markers and the bottom is the number of null markers (null meaning a score of -1 which means failure of that strain to amplify). For example: If you look at the strains AVN versus ACI, there were a total of 4,733 markers analyzed of which 1641 were mono, 2123 were poly and 969 were null (-1). Thus the two strains exhibit a polymorphism rate of 56%--(2123 / (2123 + 1641)).

Search for marker information by marker's name

Please note that the data representing the four strains used for the two mapping crosses was generated here at the WIBR/MIT CGR in a seperate experiment from the remaining 48 strains which were characterized at the Medical College of Wisconsin. Therefore, you may find that artificial polymorphisms result if you use too small a base pair tolerance when comparing one of these four strains to strains in the 48 strain group. However, within either the four strain group or the 48 strain group you may choose a tolerance of as small as you like and it should yield accurate polymorphism data.  When using the above cgi-search you will not encounter this problem as each strain is represented by the MCW data with the exceptions of SHR/MIT and BN/MIT.

For more information regarding allele sizes please contact Jo Gullings-Handley of the Jacob Lab at the Medical College of Wisconsin.

Primer sequences, original clone sequences, genetic positions and genotypes for all DNRatN and most other rat sslp's are available in various flat files by anonymous ftp.

Primer data is available in a single flat file (markers.txt) containing the lab assay name, locus name, forward and reverse primer sequences and predicted product size based on original clone sequence.

Original clone sequences for most markers are available in 42 separate files (ChrN_cross.txt) (top = SHRSP x BN; bottom = FHH x ACI) each containing the marker's locus name and clone sequence from which it was derived.

The genetic position data for each marker is available in 42 separate files (top = SHRSP x BN; bottom = FHH x ACI) containing locus name, lab assay name, placement type, and genetic distance in Kosambi centimorgans.

Genotype data for each marker is available in 42 separate files (ChrN_cross.txt) (top = SHRSP x BN; bottom = FHH x ACI) each containing the marker's locus names and genotypes for that particular cross and chromosome.

For more information regarding any of this data please contact Robert Steen.