Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 May 6;17(1):91.
doi: 10.1186/s13059-016-0953-9.

High-performance web services for querying gene and variant annotation

Jiwen Xin  1 , Adam Mark  1   2 , Cyrus Afrasiabi  1 , Ginger Tsueng  1 , Moritz Juchler  3 , Nikhil Gopal  3 , Gregory S Stupp  1 , Timothy E Putman  1 , Benjamin J Ainscough  4 , Obi L Griffith  4 , Ali Torkamani  5   6 , Patricia L Whetzel  7 , Christopher J Mungall  8 , Sean D Mooney  3 , Andrew I Su  9   10 , Chunlei Wu  11
Affiliations

High-performance web services for querying gene and variant annotation

Jiwen Xin et al. Genome Biol. .

Abstract

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

Keywords: API; Annotation; Cloud; Database; Gene; Repository; Variant.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Schematic design of the MyGene.info architecture. Colors depict different update frequencies. Small gray circles indicate multiple nodes for scalability. MyVariant.info shares the same architecture as MyGene.info except for different sets of annotation data sources and update frequencies. Additional file 2: Figure S1 shows the exact architecture of MyVariant.info
Fig. 2
Fig. 2
The demo workflow for candidate gene prioritization using MyVariant.info and MyGene.info web services. We reimplemented five filtering steps in this workflow to prioritize candidate genes from a Miller syndrome study [17]. Selected R code is displayed for each filter step, using myvariant and mygene Bioconductor packages. The number of candidate genes left at each filtering step is displayed at the left side. The full code is available at https://github.com/sulab/myvariant.info/blob/master/docs/ipynb/myvariant_R_miller.ipynb, and also in Additional file 2: Supplementary Note 1
See this image and copyright information in PMC

References

    1. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42:D749–755. doi: 10.1093/nar/gkt1196. - DOI - PMC - PubMed
    1. UniProt C. Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014;42:D191–198. doi: 10.1093/nar/gkt1140. - DOI - PMC - PubMed
    1. Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, et al. New and continuing developments at PROSITE. Nucleic Acids Res. 2013;41:D344–347. doi: 10.1093/nar/gks1067. - DOI - PMC - PubMed
    1. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42:D472–477. doi: 10.1093/nar/gkt1102. - DOI - PMC - PubMed
    1. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80. doi: 10.1186/gb-2004-5-10-r80. - DOI - PMC - PubMed

Publication types