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

Oz Solomon,Ninette Amariglio,Ortal Barel,Nitzan Kol,Raz Somech,Eran Eyal,Amos Simon,Atar Lev,Vered Kunik,Gidi Rechavi

doi:10.1186/s12864-016-3028-0

Oz Solomon, Ninette Amariglio + Show 8 more

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https://doi.org/10.1186/s12864-016-3028-0

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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.

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Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era
Solomon et al BMC Genomics (2016) 17:681. This issue is an example of the major challenge we are facing in the high throughput sequencing (HTS) era, which is to integrate efficiently and conveniently large amount of data from distinct origins
Some tools like SNPs3D [4], MutDB [5], LS-Single nucleotide polymorphisms (SNPs)/Protein data bank (PDB) [6] and Cn3D enable the user to explore variants which are stored at variant databases but not to upload new user defined variants

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Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Understanding the consequence of protein-coding point mutations is crucial to elucidate mechanisms of function and disease. This need has become even more urgent in recent years as generation sequencing technologies and downstream pipelines typically identify many mutations which should be rapidly and accurately prioritized to assess their relevance. Ball-SNP [8] for example, allows integration of UCSF chimera with Cytoscape and other resources for integrative visualization of networks, sequences and structures. These tools enable the use of more sophisticated modelling features, but are obviously, less accessible to the community. There are other good tools, like ELAPSIC [9] and SNPeffect [10] for analysis of functional, stability and protein-protein interactions changes upon point mutations which requires protein or structure information input, and do not support conversions between genomic and protein coordinates

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