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General Research Use collection streamlines access to patient-level data in dbGaP
In response to many requests from dbGaP users to simplify and streamline the data access request process while respecting patient consent, dbGaP staff have identified “General Research Use” individuals from different studies and created a collection that allows users to access data on these individuals through a single access request.
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dbVar now accepts VCF submissions of structural variation data
dbVar, NCBI's database of genomic structural variation, now accepts submissions in the Variant Call Format (VCF) in addition to their other standard formats: Excel, Tab, and XML. Instructions for submitting in VCF can be found on the dbVar Home, Submission Guidelines, and Submission Templates pages.
New NCBI Insights blog post: NCBI's medical genetics resources
The latest blog post on NCBI Insights, “NCBI’s 3 Newest Medical Genetics Resources: GTR, MedGen and ClinVar”, gives an overview of NCBI’s three medical genetics resources and outlines their content features. A more in-depth introduction is available in the Medical Genetics Resources webinar from June 2014.
NCBI webinar on E-Utilities October 15th
On October 15th, NCBI will have a webinar entitled “An Introduction to NCBI’s E-Utilities, an NCBI API.” E-Utilities is a tool to assist programmers in accessing, searching and retrieving a wide variety of data from NCBI servers.
NCBI Sequence Viewer version 3.4 available
NCBI Sequence Viewer has recently been updated and now has improved visualization of graphs, sequence track and other text, as well as a reworked configuration dialog. A full list of new features, improvements and fixes is included in the release notes.
HIV-1, human interaction database updated
The HIV-1, human interaction database has been updated and is now on an improved page. The improved interface includes help documentation and supports structured queries against Gene, as well as browsing, filtering and downloading the protein and replication interaction data sets. The most recent data release (June 2014) includes 12,785 HIV-1, human protein-protein interactions for 3,142 human genes and 1,316 replication interactions for 1,250 human genes.
Virus Variation Resource pages for Ebolavirus, MERS coronoavirus give quick and easy access to related sequences and other data
NCBI has created resource pages for Ebolavirus and MERS coronavirus, giving users an easy way to find all sequences related to these pathogens. These pages aggregate links to virus data at NCBI and also provide important links out to other information at the CDC, WHO, and HealthMap.
Simplified FASTA headers included on new NCBI Genomes FTP site
Last month, a major revision of the NCBI Genomes FTP site was announced. In response to user feedback, a new format for FASTA headers of genome, protein and transcript records has been implemented. This new format is limited to records in the /all/, /refseq/, and /genbank/ directories on the new Genomes FTP site and does not affect the Nucleotide database web FASTA displays.
RefSeq release 67 available on FTP
The full RefSeq release 67 is now available on the FTP site with over 61 million records describing 45,166,402 proteins, 8,163,775 RNAs, and sequences from 41,913 different NCBI TaxIDs.
Identical Protein Report Display option added to Protein database
A new display option has been added to the Protein database - the "Identical Protein Report". When viewing an individual record, this display allows you to access a list of all other identical proteins including those submitted as translations to GenBank, as well as RefSeq, UniProtKB/Swiss-Prot, PIR, PDB, and patented protein records.