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Genome Med. 2014 Nov 20;6(11):100. doi: 10.1186/s13073-014-0100-8. eCollection 2014.

YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens.

Author information

1
Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, Minneapolis, MN 55415 USA.
2
Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142 USA.
3
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978 Israel.
4
Department of Computer Science and Engineering, University of Minnesota, 200 Union St SE, Minneapolis, MN 55455 USA.
5
Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, Minneapolis, MN 55415 USA ; Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978 Israel.

Abstract

The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The YMAP pipeline (http://lovelace.cs.umn.edu/Ymap/) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.

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