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The SRTM digital elevation data provided on this site has been processed to fill data voids and to facilitate its ease of use by a wide group of potential users. This data is provided in an effort to promote the use of geospatial science and applications for sustainable development and resource conservation in the developing world. Digital elevation models (DEM) for the entire globe, covering all of the countries of the world, are available for download on this site.
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SQL Server Management Studio (SSMS) is an integrated environment for managing any SQL infrastructure, from SQL Server to Azure SQL Database. SSMS provides tools to configure, monitor, and administer instances of SQL Server and databases. Use SSMS to deploy, monitor, and upgrade the data-tier components used by your applications and build queries and scripts.
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Whole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here we present the latest updates to dbNSFP (version 4.1), a database designed to facilitate this step by providing deleteriousness prediction and functional annotation for all potential nonsynonymous and splice-site SNVs (a total of 84,013,093) in the human genome. The current version compiled 36 deleteriousness prediction scores, including 12 transcript-specific scores, and other variant and gene-level functional annotations. The database is available at with a downloadable version and a web-service.
Here we report the major updates of dbNSFP since version 3.0 to the current version 4.1. The core SNVs have been rebuilt based on human reference sequence version hg38 and GENCODE version 29 [14]. Compared to version 3.0 [13], dbNSFP v4.1 added 18 deleteriousness prediction scores (BayesDel_addAF and BayesDel_noAF [15], CADD_hg19 [16], ClinPred [17], DEOGEN2 [18], Eigen and Eigen PC [19], FATHMM-XF [20], GenoCanyon [21], LINSIGHT [22], LIST-S2 [23], M-CAP [24], MPC [25], MutPred [26], MVP [27], PrimateAI [28], REVEL [29], SIFT4G [30]), one score for loss of function prediction (ALoFT [31]), and three conservation scores (phyloP17way_primate [32], phastCons17way_primate [33], bStatistic [34]), making the total number of prediction scores to 46 (Additional file 1: Table S1). Many other functional annotation resources have been added or updated. In addition to the previously supported query of two attached databases, dbscSNV [35] and SPIDEX [36], for predicting splice interrupting SNVs, the companion query program for the downloadable version added support for querying SpliceAI, a third-party database for predicting splice site gain and loss [37], and dbMTS, a comprehensive database for microRNA target site SNVs and their functional predictions [38]. More importantly, much effort has been made to increase further the usability of the functional annotations, including (1) making functional predictions transcript-specific whenever possible, (2) providing transcript annotations to help to choose appropriate transcript from multiple isoforms for each gene, (3) providing HGVS (Human Genome Variation Society) c. and p. presentations of the SNVs to facilitate the query of candidate mutations reported in medical genetics literatures, and (4) providing graphic user interface for querying downloadable version as well as web-service for researchers with minimum bioinformatics training.
dbNSFP v4.1 can be accessed as either a downloadable and standalone version, or as a web-service at The standalone version is suitable for a large-scale query, such as quickly identifying nsSNVs and ssSNVs from exome sequencing studies. As no internet connection is required, maximum speed and security can be achieved. The query can be conducted via the companion Java program, which supports both the command-line and graphic user interface (GUI). The query term can be either a genomic position (chromosome, position), an SNV (chromosome, position, reference allele, alternative allele), an amino acid (AA) change (chromosome, position, reference allele, alternative allele, reference AA, alternative AA), a dbSNP ID (rs number), an HGVS c. or p. presentation of a mutation, or a gene name or ID. The companion Java program also supports searching attached databases along with dbNSFP, including dbscSNV, SPIDEX, spliceAI, and dbMTS, which helps to identify candidate disease-causing SNVs affecting splicing and miRNA binding.
The web-service, which is managed by Microsoft SQL Server 2017, is suitable for a small-scale query such as obtaining functional annotations for candidate SNVs. By submitting one or multiple genome coordinates (chromosome, position, reference allele, and alternate allele), users can easily retrieve all the annotation columns in dbNSFP. The output will be displayed on the web page and available as a downloadable TAB-delimited text file for further filtering.
In conclusion, we present dbNSFP v4, a significant improvement over v3 over the past 4 years, as to supporting transcript-specific predictions and annotations, convenience to use (GUI support, joint-query of attached databases, and web-service), and double the number of deleteriousness prediction scores as to nsSNV. dbNSFP will continue to serve the community of medical geneticists as to providing comprehensive and easily-accessible tools for functional annotations and predictions for SNVs that cause amino acid changes and splicing changes.
The web service of dbNSFP v4 can be found at The downloadable version of dbNSFP v4 can be found at and All data sources and websites for downloading can be found in Additional file 1: Table S1. dbNSFP v4 is also available at and
X.L. designed the study, constructed the database, wrote the query program for the downloadable version, and attached databases. C.L. conducted analyses of the prediction scores. C.M., Y.D., and C.T. developed the web-service. X.L., C.L., and C.M. wrote the manuscript. All authors read and approved the final manuscript.
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Percona Monitoring and Management (PMM) is an open source observability, monitoring, and management tool for MySQL, PostgreSQL, and MongoDB. With PMM, you can easily monitor the health of your database infrastructure, explore new patterns in database behavior, and manage and improve the security of your databases no matter where they are located or deployed, without lock-in.
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Update 2015.11.05: Version 4.1 GWAS and eQTL have been updated; a simpler pruning strategy is applied when combining GWAS; and links out to other NHGRI/EBI GWAS hits and GRASP QTL hits are provided.Update 2015.09.15: Version 4.0 now includes many recent eQTL results including the GTEx pilot, four different options for defining enhancers using Roadmap Epigenomics data, and a complete set of source files for download and local analysis. Older versions available: v3, v2, v1.
Security is #1 priority in development of Adminer. Adminer does not allow connecting to databases without a password and it rate-limits the connection attempts to protect against brute-force attacks. Still, consider making Adminer inaccessible to public by whitelisting IP addresses allowed to connect to it, password-protecting the access in your web server, enabling security plugins (e.g. to require an OTP) or by customizing the login method. You can also delete Adminer if not needed anymore, it is just one file which is easy to upload in the future. Adminer had some security bugs in the past so update whenever Adminer tells you there is a new version available (ask your administrator if you could not update yourself).
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