Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system

• Published in: BMC genetics Vol. 13; no. 1; p. 24
• Main Authors: Curtis, Ross E, Goyal, Anuj, Xing, Eric P
• Format: Journal Article
• Language: English
• Published: London BioMed Central 03.04.2012; Springer Nature B.V; BMC
• Subjects: Algorithms; Animal Genetics and Genomics; Automation; Biomedical and Life Sciences; Chromosome Mapping - methods; Computer programs; Gene expression; Gene mapping; Gene polymorphism; Genetic Association Studies; Genetics; Genetics and Population Dynamics; Genomes; Life Sciences; Microbial Genetics and Genomics; Plant Genetics and Genomics; Population structure; Programming languages; Software; Studies; Visualization; Pittsburgh Pennsylvania; Association Result; Association Mapping; Processing Pipeline; Lasso; Gene Expression Measurement
• ISSN: 1471-2156; 1471-2156
• DOI: 10.1186/1471-2156-13-24

Background Structured association mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required to use these cutting-edge techniques, geneticists often revert to simpler, less powerful methods. Results To make structured association mapping more accessible to geneticists, we have developed an automatic processing system called Auto-SAM. Auto-SAM enables geneticists to run structured association mapping algorithms automatically, using parallelization. Auto-SAM includes algorithms to discover gene-networks and find population structure. Auto-SAM can also run popular association mapping algorithms, in addition to five structured association mapping algorithms. Conclusions Auto-SAM is available through GenAMap, a front-end desktop visualization tool. GenAMap and Auto-SAM are implemented in JAVA; binaries for GenAMap can be downloaded from http://sailing.cs.cmu.edu/genamap .