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Bioinformatics. 2011 Feb 1;27(3):416-8. doi: 10.1093/bioinformatics/btq658. Epub 2010 Dec 12.

MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.

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Department of Biological and Biomedical Sciences, Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA.


Next-generation sequencing technologies enable the identification of sequence variation in the genome and transcriptome. Differences between the reference genome and transcript libraries complicate the determination of the effect of genomic sequence variants on protein products; similarly, these differences complicate the mapping of sequence variants found in transcripts to their respective genomic position. We have developed MU2A, a publicly available web service for variant annotation that reconciles differences between the genome and transcriptome, enabling the rapid and accurate determination of the effects of genomic variants on protein products, and the mapping of variants detected in transcripts to genomic coordinates. The MU2A web service is available at We have released MU2A as open source, available at

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