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

Franz Rüschendorf; Peter Nürnberg

doi:10.1093/bioinformatics/bti264

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

Bioinformatics. 2005 May 1;21(9):2123-5. doi: 10.1093/bioinformatics/bti264. Epub 2005 Jan 12.

Authors

Franz Rüschendorf¹, Peter Nürnberg

Affiliation

¹ Bioinformatics Department, Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine Berlin-Buch, Germany. [email protected]

PMID: 15647291
DOI: 10.1093/bioinformatics/bti264

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/

Publication types

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

MeSH terms

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