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

Abstract

BackgroundThe 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.ResultsSeqAnt (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.ConclusionSeqAnt 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.

Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte–Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn’s Disease

“…genetics.emory.edu/), which reports the variant's functional classification (nonsense, replacement, silent, 5' or 3' UTR, intronic, intergenic), presence in databases including dbSNP, and Combined Annotation-Dependent Depletion (CADD) scores. 14,15 We used the Exome Aggregation Consortium (ExAC) reference data set for estimation of allele frequency (http://exac.broadinstitute.org/).…”

SeqAnt 2012: Recent Developments in Next-Generation Sequencing Annotation

“…Since the initial publication of SeqAnt, we made a number of improvements that have been incorporated into SeqAnt 2.0 [5]. These modifications fall into four main categories.…”

“…On the home page, we eliminated redundant tabs and buttons, simplified the overall design, and upgraded the graphic interface's color scheme (Figure 1). This page includes basic information about the original publication of SeqAnt [5], a link to contact the Zwick laboratory, and the web URL for the the SourceForge website (http://seqant.sourceforge.net), where the source code and associated binary libraries can be freely downloaded. From this page, the user is able to quickly access the three main types of input data accepted by SeqAnt.…”

“…Single nucleotide variants (SNVs) and small insertions and deletions (INDELs) were annotated using SeqAnt [5]. For the SNPs, a total of 68, or 39%, had not been reported before (31 in NLGN3 and 37 in NLGN4X, Table 2).…”

“…To address this problem, we developed the Sequence Annotator (SeqAnt, http://seqant.genetics.emory.edu/), 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 [5]. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation.…”