June 27 NCBI Minute: dbGaP’s New Ancestry Composition Visualization tool and GRAF Software

Next Wednesday, June 27, 2018, we’ll introduce you to the Genetic Relationship and Fingerprinting (GRAF) software package. GRAF is a quality assurance tool that finds duplicates and closely related subjects in your data using SNP genotypes. We’ll also introduce the … Continue reading

April and May annotations in RefSeq: cow, bonobo and more

In April and May, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms: Bos taurus (cattle) Cephus cinctus (wheat stem sawfly) Citrus sinensis (sweet orange) Cynara cardunculus cardunculus (eudicot) Cynoglossus semilaevis (tongue sole) Gallus … Continue reading

Improvements made to genomes FTP site

We’ve been making improvements to the contents of NCBI’s genomes FTP site. Highlights include: addition of new file types, including a feature_count.txt file with counts of gene, RNA, and CDS features of specific types and a translated_cds.faa file with conceptual … Continue reading

Summer 2018 NIH Data Hackathon July 23-25, 2018

From July 23rd to 25th, 2018, NCBI will host a data science hackathon on the NIH campus. This hackathon will focus on genomics as well as general Data Science analyses including text, image and sequence processing. This event is for … Continue reading

Improved annotation of Streptomyces RefSeq genomes

We’ve completed the RefSeq reannotation of over 1,000 Streptomyces genomes! The genomes were reannotated using the Prokaryotic Genome Annotation Pipeline (PGAP). PGAP detected nearly 100% of ribosomally synthesized and post-translationally modified peptide natural products (RiPP)-encoding genes from known families, despite … Continue reading

Important dbSNP updates: New JSON data files, RefSNP report, API

dbSNP is moving to the new design with new products ready for testing including new JSON data files, the RefSNP page, and an API. New JSON data files Human Build 151 release is the last build that will provide relational … Continue reading

5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more

Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos. NCBI Minute: Getting the Most out of Web BLAST Tabular Format The NCBI web BLAST service has several useful download formats, including tabular formats. … Continue reading

June 20 NCBI Minute: Getting the Genomic Context for BLAST Protein Matches

Do you ever want to see the flanking genes of a protein match from a BLAST search?  On June 20th, we’ll show you how to see the genomic context of bacterial proteins using the identical protein report and the graphical … Continue reading

dbVar Structural Variation Non-redundant Reference Sets (Alpha) Release

dbVar has generated known structural variants (SV) datasets for use in comparisons with user data to aid variant calling, analysis and interpretation. Files containing Non-Redundant (NR) deletions, insertions, and duplications are now available on GitHub. Additional separate files include preliminary … Continue reading

June 13 NCBI Minute: Using EDirect to Query a Local Installation of PubMed

Next Wednesday, June 13, 2018, we’ll show you how to use EDirect to install PubMed locally and then search and retrieve records from the local instance. You will also see an analysis example that shows the significant speed improvement with … Continue reading