ALOHOMORA: a tool for linkage analysis using 10K SNP array data.
basic_science · Level V
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Abstract
ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire dataset as well as for individual families. ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/
Medical subject headings
- Chromosome Mapping
- DNA Mutational Analysis
- Linkage Disequilibrium
- Oligonucleotide Array Sequence Analysis
- Polymorphism, Single Nucleotide
- Software
- User-Computer Interface