G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures

BMC Genomics

Software

Eran Eyal¹  Nitzan Kol¹  Ortal Barel¹  Vered Kunik¹  Gidi Rechavi²  Oz Solomon³  Ninette Amariglio³  Raz Somech⁴  Amos Simon⁵  Atar Lev⁵ 

[1] Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel;Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel;Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel;Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel;The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel;Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel;Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel;Pediatric Immunology Service, Jeffrey Modell Foundation, Sheba Medical Center, Ramat-Gan, Israel;

关键词: Variant;    Mutation;    Structure;    Protein;    Visualization;   

DOI  :  10.1186/s12864-016-3028-0

 received in 2016-05-24, accepted in 2016-08-19,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundEvaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates.ResultsWe present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D.ConclusionsG23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

【 授权许可】

CC BY   
© The Author(s). 2016