LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.
| Title: | LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. |
|---|---|
| Authors: | Hao K; Algorithm and Data Analysis, Affymetrix Inc. 3420 Central Expressway, Santa Clara, California, USA. ke_hao@affymetrix.com; Di X; Cawley S |
| Source: | Bioinformatics (Oxford, England) [Bioinformatics] 2007 Jan 15; Vol. 23 (2), pp. 252-4. Date of Electronic Publication: 2006 Dec 05. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford : Oxford University Press, c1998- |
| MeSH Terms: | Software*; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; Genetic Markers/*genetics ; Linkage Disequilibrium/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA/*methods; Genetic Variation/genetics ; Sequence Alignment/methods ; Algorithms ; Base Sequence ; Molecular Sequence Data ; Statistics as Topic |
| Abstract: | Unlabelled: The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations.; Availability: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx |
| Substance Nomenclature: | 0 (Genetic Markers) |
| Entry Date(s): | Date Created: 20061207 Date Completed: 20070306 Latest Revision: 20220311 |
| Update Code: | 20260130 |
| DOI: | 10.1093/bioinformatics/btl574 |
| PMID: | 17148510 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't