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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/

Links

  • FREE Publisher Full Text
  • 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

    Citation

    TY - JOUR T1 - ALOHOMORA: a tool for linkage analysis using 10K SNP array data. AU - Rüschendorf,Franz, AU - Nürnberg,Peter, Y1 - 2005/01/12/ PY - 2005/1/12/aheadofprint PY - 2005/1/14/pubmed PY - 2005/8/24/medline PY - 2005/1/14/entrez SP - 2123 EP - 5 JF - Bioinformatics (Oxford, England) JO - Bioinformatics VL - 21 IS - 9 N2 - 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/ SN - 1367-4803 UR - https://www.unboundmedicine.com/medline/citation/15647291/ALOHOMORA:_a_tool_for_linkage_analysis_using_10K_SNP_array_data_ L2 - http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15647291 ER -