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April 26th NCBI Minute: Medical Genetics Summaries on the NCBI Bookshelf - a pharmacogenomics resource for clinicians

Wednesday, April 19, 2017

Next Wednesday, April 26, 2017, NCBI staff will introduce the Medical Genetics Summaries, a growing collection of reviews available on the NCBI Bookshelf. Each chapter of this book highlights the impact of genetic variations on response to drugs (pharmacogenomics). By the end of this NCBI Minute, you will be able to use the Medical Genetics Summaries to find information about a particular drug, including known impacts of genetic variation on drug response (efficacy, toxicity, side effects) and identify actionable information, including information about relevant genetic testing and how to interpret the test results in order to optimize therapy based on a patient's genotype.

Maize (Zea mays) genome annotation release 101 is now available!

Wednesday, April 12, 2017

A new maize (Zea mays) genome annotation has been produced by the RefSeq eukaryotic genome annotation pipeline. In Annotation Release 101 a total of 47,446 genes were annotated, including 37,380 that code for proteins. This data is now available for download and can be explored in the Genome Data Viewer, with BLAST, and in the Gene database.

dbSNP FTP file format change planned for early 2018

Tuesday, April 11, 2017

In early 2018, dbSNP will no longer provide relational database table dumps on the FTP site or any general SQL support for future build releases. Instead, dbSNP FTP data will be made available as a cumulative file of RefSNP objects in JSON format. These files are now available, so users can begin migration and testing. Please see the dbSNP Alert README file for more details.

dbSNP's human build 150 has doubled the amount of RefSNP records!

Tuesday, April 11, 2017

dbSNP’s Human Build 150 includes a large number of new submissions from the Human Longevity, Inc. (HLI) and TopMed, increasing the total number of Human RefSNPs in the database from 154 to 324 million. TopMed has also provided new allele frequency data for 163 million RefSNPs.

NCBI researchers and collaborators discover novel group of giant viruses

Thursday, April 6, 2017

Nearly complete set of translation-related genes lends support to hypothesis that giant viruses evolved from smaller viruses

April 19th NCBI Minute: Magic-BLAST, NCBI's next-gen sequence alignment program

Wednesday, April 5, 2017

In two weeks, NCBI staff will introduce you to Magic-BLAST, NCBI's next-gen sequence aligner. You will learn to use magic-BLAST to align next-gen RNA and DNA sequencing runs to genomic and transcript sequences and to understand the options available for magic-BLAST

Six functional prototypes available from the March NCBI hackathon

Wednesday, April 5, 2017

At the March 2017 NCBI Genomics Hackathon, participants developed six functional software prototypes, several of which are still under active development. Software is available from the NCBI-Hackathons GitHub site.

Eight new eukaryotic genome annotations added to RefSeq

Tuesday, April 4, 2017

In the past month, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:

New Genome Data Viewer access page

Monday, April 3, 2017

NCBI is pleased to offer a direct entry point to the NCBI Genome Data Viewer (GDV) that supports the exploration, visualization and analysis of eukaryotic RefSeq genome assemblies. The new GDV homepage includes an interactive interface for a quick overview of supported organisms, specific genome searches plus inter-connectivity to Assembly and RefSeq annotation resources. About 100 genome assemblies are now ready for GDV exploration with more on the way. Stay tuned!

Sequence Viewer 3.20 is now available

Thursday, March 30, 2017

Sequence Viewer 3.20 has several new features, improvements and bug fixes, including discrete color maps for graph tracks, improved performance in initialization and loading tracks, improved display of overlapping variation features and the addition of a status bar. For a full list of changes, see the Sequence Viewer release notes.

Conserved Domain Database (CDD) version 3.16 now available online and via FTP

Thursday, March 30, 2017

Version 3.16 of the Conserved Domain Database contains 1,659 new or updated NCBI-curated domains (56,066 total), including models specifically built to annotate structural motifs (accession prefix "sd"), and now mirrors Pfam version 30.

NCBI to assist with BioFrontiers Hackathon in May

Monday, March 27, 2017

From May 22nd to 24th, NCBI will be assisting with the BioFrontiers Hackathon in Boulder, Colorado. Please see the BioFrontiers Hackathon website for more information, including what to expect, who should apply, and the application itself. Applications are due by April 7, 2017.

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