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ALOHOMORA: a tool for linkage analysis using 10K SNP array data.

Abstract

SUMMARY

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.

AVAILABILITY

ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/

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  • Authors

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    Source

    Bioinformatics (Oxford, England) 21:9 2005 May 1 pg 2123-5

    MeSH

    Algorithms
    Chromosome Mapping
    Computer Graphics
    DNA Mutational Analysis
    Gene Frequency
    Genetics, Population
    Humans
    Linkage Disequilibrium
    Oligonucleotide Array Sequence Analysis
    Polymorphism, Single Nucleotide
    Software
    User-Computer Interface

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    15647291