(********************************************************************* GeneticSymbols.m Symbols used for representing genetic phenotypes in the Simulation and SegregationAnalysis packages. \[Copyright] copyright Kenneth F. Manly, 1998,1999 Package design adapted from Roman E. Maeder: Programming in Mathematica, Second Edition, Addison-Wesley, 1991. *********************************************************************) (*:Title: GeneticSymbols *) (*:Author: Kenneth F. Manly*) (*:Copyright: \[Copyright] copyright Kenneth F. Manly, 1998 *) (*:Package Version: 2.2 *) (*:Mathematica Version: 3.0 *) (*:Summary: Symbols used in other packages for generating simulated genetic mapping data from backcrosses or intercrosses including quantitative trait data, and for analyzing simulated or actual mapping data. *) (*:Keywords: biology, genetics, simulations, mapping, backcross, intercross, quantitative trait *) (*:Discussion: These codes are used in various functions to specify the genetic segregation pattern in a population or at a locus. BC0 and BC1 specify two different cases of a backcross pattern with codominant markers (maternal-recurrent and paternal-recurrent, respectively). BD0 and BD1 similarly specify the same cases of a backcross pattern with a dominant marker (maternal-recurrent/paternal-dominant and paternal-recurrent/maternal-dominant, respectively). BC0 and BC1 cannot both appear in the progeny of a backcross or intercross of inbred lines; similarly for BD0 and BD1. Both members of either pair may appear in the progeny of non-inbred parents. When a pair of loci show BC0 and BC1 patterns (or BD0 and BD1 patterns), the segregation gives no information about recombination between the loci. IC specifies a intercross pattern with codominant markers, and ID0 and ID1 specify two different cases of an intercross pattern with a dominant marker (paternal-dominant and maternal-dominant, respectively). DH specifies the segregation pattern of doubled haploid lines. RI, Self, and Sib refer to sets of recombinant inbred lines. Self and Sib refer to sets created by self-mating and sib-mating, respectively. RI is used in cases where the type of recombinant inbred set does not make a difference. *) (*:Context: Genetics`GeneticSymbols` *) (*:Source: Kenneth F. Manly, PhD, Molecular & Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, 14263-0001 *) (*:History: 8/98 Add radiation hybrids 4/99 Add advanced intercross 4/99 Add advanced backcross *) (*:Limitations: *) BeginPackage["Genetics`GeneticSymbols`"]; BC0::usage = "The symbol BC0 specifies a codominant maternal-recurrent backcross segregation, using the symbols A and H."; BC1::usage = "The symbol BC1 specifies a codominant paternal-recurrent backcross segregation, using the symbols B and H."; BD0::usage = "The symbol BD0 specifies a maternal-recurrent, paternal-dominant backcross segregation, using the symbols A and C."; BD1::usage = "The symbol BD1 specifies a paternal-recurrent, maternal-dominant backcross segregation, using the symbols B and D."; ABC0::usage = "The symbol ABC0 specifies a codominant maternal-recurrent advanced backcross segregation, using the symbols A and H."; ABC1::usage = "The symbol ABC1 specifies a codominant paternal-recurrent advanced backcross segregation, using the symbols B and H."; ABD0::usage = "The symbol ABD0 specifies a maternal-recurrent, advanced paternal-dominant backcross segregation, using the symbols A and C."; ABD1::usage = "The symbol ABD1 specifies a paternal-recurrent, advanced maternal-dominant backcross segregation, using the symbols B and D."; IC::usage = "The symbol IC specifies a codominant intercross segregation, using the symbols A, H, and B."; AIC::usage = "The symbol AIC specifies a codominant advanced intercross segregation, using the symbols A, H, and B."; ID0::usage = "The symbol ID0 specifies a paternal-dominant intercross segregation, using the symbols A and C."; ID1::usage = "The symbol ID1 specifies a maternal-dominant intercross segregation, using the symbols B and D."; AID0::usage = "The symbol AID0 specifies a paternal-dominant advanced intercross segregation, using the symbols A and C."; AID1::usage = "The symbol AID1 specifies a maternal-dominant advanced intercross segregation, using the symbols B and D."; DH::usage = "The symbol DH specifies a segregation such as found in doubled haploid lines, using the symbols A and B."; RI::usage = "The symbol RI specifies a segregation such as found in recombinant inbred lines, using the symbols A and B."; Self::usage = "The symbol Self specifies a selfed recombinant inbred population."; Sib::usage = "The symbol Sib specifies a sib-mated recombinant inbred population."; QTB::usage = "The symbol QTB specifies the effect of a quantitative trait locus in a backcross. Use QTI for an intercross."; QTI::usage = "The symbol QTI specifies the effect of a quantitative trait locus in an intercross or RI lines. Use QTB for an backcross."; RH::usage = "The symbol RH specifies a recombinant hybrid segregation, using the symbols A and B"; A::usage = "The symbol A is used in progeny distribution patterns to indicate a maternal phenotype and in radiation hybrids to indicate presence of a marker."; H::usage = "The symbol H is used in progeny distribution patterns to indicate a heterozygous phenotype."; B::usage = "The symbol B is used in progeny distribution patterns to indicate a paternal phenotype and in radiation hybrids to indicate absence of a marker."; C::usage = "The symbol C is used in progeny distribution patterns to indicate a not-maternal phenotype. This indicates that the paternal phenotype is known to be dominant, and that the observed genotype is either paternal or heterozygous."; D::usage = "The symbol D is used in progeny distribution patterns to indicate a not-paternal phenotype. This indicates that the maternal phenotype is known to be dominant, and that the observed genotype is either maternal or heterozygous."; U::usage = "The symbol U is used in progeny distribution patterns to indicate an unknown phenotype, added by the Ambiguate function."; Protect[BC0, BC1, BD0, BD1, ABC0, ABC1, ABD0, ABD1, IC, AIC, ID0, ID1, AID0, AID1, DH, QTB, QTI, RI, Self, Sib, RH, A, H, B, C, D, U]; EndPackage[]