Note: This post, originally published in June 2018, was updated in November 2020.
dbNSFP(v4.1) is an integrated database of functional annotations for the human genome which compiles data from multiple sources to provide highly distilled information at both the variant* and gene level. The dbNSFP gene level annotation table can be imported into ArrayStar, part of Lasergene Genomics, and accessed within the gene table, as well as used for advanced filtering.
*Note that for analysis at the variant level, Lasergene Genomics offers a unique variant annotation database, which includes data from dbNSFP such as ClinVar and Sift predictions, as well as literature citations from Mastermind, and allele and genotype frequencies from the 1000 Genomes Project.
To use dbNSFP annotations in ArrayStar:
- Download the following zipped file: dbNSFP4.1_gene.zip
- Decompress the zipped file.
- Open your ArrayStar project, choose File>Import Annotations and select the dbNSFP4.1_gene file from the decompressed dbNSFP folder.
Note: To add GO annotations to your dbNSFP annotation data, select the Data>Download Annotations… menu command.
References
- Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Human Mutation. 32:894-899.
- Liu X, Wu C, Li C and Boerwinkle E. 2016. dbNSFP v3.0: A One‐Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice‐Site SNVs. Human Mutation. 37:235-241.
- Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, and Liu X. (2015) Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Human Molecular Genetics. 24(8):2125-2137.
- dbNSFP Database at the Jpopgen website.
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