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 sequence viewer. You will also learn to use these reports in detail and how to get these genomic contexts in batch for a set of protein matches using the identical proteins report and EDirect .

Date and time: Wed, June 20, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

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 annotations of overlap with ACMG59 genes. All files are in tab-delimited text format.

We encourage you to test these files and provide feedback, either on GitHub or by email.

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 the Local Cache and employs some advanced EDirect xtract options to aid with processing records.

Date and time: Wed, June 13, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Formulas will be displayed in PubMed Titles and abstracts


Starting this month, we will begin displaying formulas in citation titles, abstracts and keywords in PubMed.

Previously, formulas were replaced with “[Formula: see text]” (see Figure 1).

PubMed abstract display without formula

Figure 1. Formula replaced with [Formula: see text] in the PubMed abstract display.

With this enhancement, you will now see formulas in the PubMed summary and abstract displays when these data are available in new citations (see Figure 2).

PubMed abstract showing chemical formula

Figure 2. Formula shown in the PubMed abstract display after June 1, 2018.

We will also be including the MathML 3.0 element tags in PubMed XML. To support the addition of MathML tagging in our XML, we have created a DTD, which you can download now. Existing content will be valid against the new DTD. You can also download sample XML files with MathML 3.0 tags.

New dbVar FTP Directory Structure


NCBI’s database of structural variation, dbVar has a restructured FTP directory. The old directories can be found in archive.

Highlights include:

  • added aggregated vcf files by assembly
  • named files based on major assembly and region or call
  • replaced study-specific directories with file-type directories
  • renamed “.tab” files to “.tsv”
  • moved old human and all non-human files to archive

Refer to README.ftp for full details of the new GVF, VCF, TSV, and XML files.

Tour the NCBI’s Genome Data Viewer, Bookshelf, Pathogen Isolates Detection Browser and other resources on YouTube


Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.

NCBI’s Genome Data Viewer – Introducing the BLAST Widget

A brief introduction into how the BLAST widget, a new addition to the Genome Data Viewer, helps you see your BLAST results in the context of assembled genome sequences.

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