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Predicting the effects of frameshifting indels

Jing Hu1 and Pauline C Ng2*

Author Affiliations

1 Department of Mathematics and Computer Science, Franklin and Marshall College, 415 Harrisburg Ave, Lancaster, PA 17603, USA

2 Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore, Singapore 138672

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Genome Biology 2012, 13:R9  doi:10.1186/gb-2012-13-2-r9

Published: 9 February 2012

Abstract

Each human has approximately 50 to 280 frameshifting indels, yet their implications are unknown. We created SIFT Indel, a prediction method for frameshifting indels that has 84% accuracy. The percentage of human frameshifting indels predicted to be gene-damaging is negatively correlated with allele frequency. We also show that although the first frameshifting indel in a gene causes loss of function, there is a tendency for the second frameshifting indel to compensate and restore protein function. SIFT Indel is available at http://sift-dna.org/www/SIFT_indels2.html webcite