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

• Type of Material: Article
• Authors: Amol Carl Shetty, Emory University; Prashanth Athri, Emory University; Kajari Mondal, Emory University; Vanessa L. Horner, Emory University; Karyn Meltz Steinberg, Emory University; Viren Patel, Emory University; Tamara Caspary, Emory University; David J Cutler, Emory University; Michael Zwick, Emory University
• Language: English
• Date: 2010-09-20
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2010 Shetty et al; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biomedcentral.com/1471-2105/11/471
• Title of Journal or Parent Work: BMC Bioinformatics
• ISSN: 1471-2105
• Volume: 11
• Issue: 471
• Start Page: 1
• End Page: 8
• Grant/Funding Information: This work was supported in part by the National Institutes of Health/National Institute of Mental Health and Gift Fund [grant number MH076439] to MEZ, the Simons Foundation Autism Research Initiative [MEZ], and the PHD Grant (UL1 RR025008, KL2 RR025009 or TL1 RR025010) from the Clinical and Translational Science Award program, National Institutes of Health, National Center for Research Resources.
• Research Categories: Biology, Genetics

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.