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


CONCLUSIONS
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.
Shetty
Amol Carl
AC
Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
Athri
Prashanth
P
Mondal
Kajari
K
Horner
Vanessa L
VL
Steinberg
Karyn Meltz
KM
Patel
Viren
V
Caspary
Tamara
T
Cutler
David J
DJ
Zwick
Michael E
ME
D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software