Introduction

The recent advancement of the next generation sequencing technology has enabled the fast and low-cost detection of all genetic variants spreading across entire human genomes, making the application of whole-genome sequencing a tendency in studies of disease-causing genetic variants. Nevertheless, there still lacks a repository that collects predictions of functionally damaging effects of human genetic variants, though it has been well recognized that such predictions plays a central role in the analysis of whole-genome sequencing data.

To fill in this gap, we developed dbWGFP (a database of human whole-genome single nucleotide variants and their functional predictions) that contains functional predictions and annotations of more than 8.5 billion possible human whole-genome single nucleotide variants. Specifically, this database integrates 32 functional predictions calculated by 13 popular computational methods, 15 conservation features derived from 4 conservation calculation approaches, and 44 valuable annotations obtained from the ENCODE project, accompanied with a highly efficient search program.

dbWGFP offers two web services for retrieving predictions and annotations for human whole-genome single nucleotide variants. In the step-by-step mode, you can upload a file containing variants and retrieve results online. In the batch mode, you can upload a file containing your email address and variants and retrieve results via your email.

dbWGFP offers two versions for downloading. The lite version includes prediction scores for human whole-genome single nucleotide variants. The full version includes both predictions and annotations. Both versions include a search program that can extract predictions and/or annotations in a highly efficient way. Different versions of dbWGFP are also archived for easy access.

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Please cite: Jiaxin Wu, Lianshuo Li, Mengmeng Wu, Zhuo Liu, Wanwen Zeng, Rui Jiang*, dbWGFP: a database of human whole-genome single nucleotide variants and their functional predictions, Database: the journal of biological databases and curation, in revision, 2015.