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Open Access Highly Accessed Software

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

Amol Carl Shetty1, Prashanth Athri1, Kajari Mondal1, Vanessa L Horner1, Karyn Meltz Steinberg12, Viren Patel1, Tamara Caspary1, David J Cutler1 and Michael E Zwick1*

Author Affiliations

1 Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA

2 Graduate Program in Population Biology, Ecology and Evolution, Emory University, Atlanta, GA, USA

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BMC Bioinformatics 2010, 11:471  doi:10.1186/1471-2105-11-471

Published: 20 September 2010

Abstract

Background

The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research.

Results

SeqAnt (Sequence Annotator) is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds.

Conclusion

SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.