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MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
Background: various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form.

Results: we have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection.

Conclusion: MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.
1471-2105
227
Gaunt, Tom R
28c4a0b7-ec5e-4ee8-85eb-6d03b24bd6d1
Rodriguez, Santiago
f235ea2b-b6f3-45e4-9fc3-5a0383689ed6
Zapata, Carloo
7c0f070a-d458-43b4-9494-527aeecfc27e
Day, Ian N.M.
b749b30a-1f4c-40eb-af0e-a50427388b39
Gaunt, Tom R
28c4a0b7-ec5e-4ee8-85eb-6d03b24bd6d1
Rodriguez, Santiago
f235ea2b-b6f3-45e4-9fc3-5a0383689ed6
Zapata, Carloo
7c0f070a-d458-43b4-9494-527aeecfc27e
Day, Ian N.M.
b749b30a-1f4c-40eb-af0e-a50427388b39

Gaunt, Tom R, Rodriguez, Santiago, Zapata, Carloo and Day, Ian N.M. (2006) MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers. BMC Bioinformatics, 7, 227. (doi:10.1186/1471-2105-7-227).

Record type: Article

Abstract

Background: various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form.

Results: we have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection.

Conclusion: MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.

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Published date: 27 April 2006

Identifiers

Local EPrints ID: 40693
URI: http://eprints.soton.ac.uk/id/eprint/40693
ISSN: 1471-2105
PURE UUID: 83bd4300-d444-40a0-a151-714c6148803f

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Date deposited: 06 Jul 2006
Last modified: 15 Mar 2024 08:21

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Contributors

Author: Tom R Gaunt
Author: Santiago Rodriguez
Author: Carloo Zapata
Author: Ian N.M. Day

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