1Tom R. Gaunt, 1Santiago Rodriguez, 2Carlos Zapata, 1Ian N.M. Day
1Human Genetics Division, University of Southampton, School of Medicine, Duthie Building (MP808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK, 2Departamento de Genetica, Universidad de Santiago, Santiago de Compostela, Spain
Various software tools are available for the analysis and visualisation of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website (based on their data). Most graphical representations use a colour to indicate magnitude of a statistic for each pairwise analysis. Whilst this is useful over long ranges of many markers, the total information available graphically is limited.
We have developed an alternative program called MIDAS which calculates and displays an enhanced graphical representation of linkage disequilibrium. In addition to D' and significance values, haplotype frequencies (expected and estimated) are displayed and distance between markers is shown on a map. Statistics can be viewed by mouse-over for each pairwise analysis, and all data can be exported in tabular form for analysis in other programs. MIDAS is capable of analysing data from biallelic and multiallelic markers (including multi-locus haplotypes).
This program therefore facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different markers and inferences about patterns of evolution and selection.
http://www.oege.org/software/midas
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