title: VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era.
abstract: VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/) has been vastly improved since its former publication GenoWatch in the 2008 Web Server Issue. It is now at least 10 000-times faster in annotating a variant. Drastic speed increase, through complete re-design of its working mechanism, makes VarioWatch capable of annotating millions of human genomic variants generated from next generation sequencing in minutes, if not seconds. While using MegaQuery of VarioWatch to quickly annotate variants, users can apply various filters to retrieve a subgroup of variants according to the risk levels, interested regions, etc. that satisfy users' requirements. In addition to performance leap, many new features have also been added, such as annotation on novel variants, functional analyses on splice sites and in/dels, detailed variant information in tabulated form, plus a risk level decision tree regarding the analyzed variant. Up to 1000 target variants can be visualized with our carefully designed Genome View, Gene View, Transcript View and Variation View. Two commonly used reference versions, NCBI build 36.3 and NCBI build 37.2, are supported. VarioWatch is unique in its ability to annotate comprehensively and efficiently millions of variants online, immediately delivering the results in real time, plus visualizes up to 1000 annotated variants.
authors.affiliation: National Center for Genome Medicine and Institute of Biomedical Sciences, Academia Sinica, Taiwan 11529, R.O.C.
authors.forename: Yu-Chang
authors.initials: YC
authors.lastname: Cheng
authors.forename: Fang-Chih
authors.initials: FC
authors.lastname: Hsiao
authors.forename: Erh-Chan
authors.initials: EC
authors.lastname: Yeh
authors.forename: Wan-Jia
authors.initials: WJ
authors.lastname: Lin
authors.forename: Cheng-Yang Louis
authors.initials: CY
authors.lastname: Tang
authors.forename: Huan-Chin
authors.initials: HC
authors.lastname: Tseng
authors.forename: Hsing-Tsung
authors.initials: HT
authors.lastname: Wu
authors.forename: Chuan-Kun
authors.initials: CK
authors.lastname: Liu
authors.forename: Chih-Cheng
authors.initials: CC
authors.lastname: Chen
authors.forename: Yuan-Tsong
authors.initials: YT
authors.lastname: Chen
authors.forename: Adam
authors.initials: A
authors.lastname: Yao
mesh_terms: D014644:Genetic Variation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D012984:Software