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Mapping Software

Autozygosity mapping

This set of web pages contains programs that analyse Affymetrix SNP chip data files for regions of IBD. AutoSNPa concentrates on files from groups of individuals that are assumed to have the same haplotype. Where as IBDfinder makes no assumptions about haplotypes and can screen individuals from different ethnic groups as well as data from different SNP microarray datasets. Sample requires data from a number of nuclear familes and while each of the nuclear families doesn't have to have a common haplotype, all the families must have mutations in the same gene. The main feature of Sample is that it doesn't require genotype data from affected people, just the parents and siblings of affected individuals. this makes it possible to analyse embroyonic lethal mutations.

  • AutoSNPa is a program that analysis SNP data from pedigrees with multiple affected individuals.
  • AutoSNPa is a program designed to display an individual's autozygous regions next to an ideogram of the human genome.
  • IBDelphi is a program for identifying segments of IBD between two individuals and calculating the risk that a couple will have a child affected by a autosomal recessive disease.
  • IBDfinder analysis SNP data from affected individuals from different pedigree who have novel mutations in the same gene.
  • The Inbreeding calculator page contains a link to two programs. C2T converts a Cyrillic file to a text file, which can then be imported in to the CofI program to calculate the coefficient of inbreeding of members of the pedigree. Since CofI can use any suitably formatted pedigree the program was also used a the basis of a web page with the same functionality.
  • SAMPLE is a program that identifies homozygous regions linked to a disease phenotype, but unlike AutoSNPa and Ibdfinder, it does not require data from affected individuals.
Dominant Mapping

This set of programs is designed to map genes with a dominant mode of inheritance.

  • DominantMapper, this program was created to map disease genes that show a dominant mode of inheritance in related nuclear families.
  • PoD, this program was developed to identify regions linked to a dominant disease gene using SNP data from pooled DNA samples. However the method does not seem to work.
Copy number analysis

This program is designed to map genes which are affected by variations in copy number.

  • CNViewer, this program was created to map copy number variation that is common to affected individuals, but absent from health individuals.
Mapping file formating software

The section contains applications that convert different genotyping file formats to those that the software on this page can use.

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