September 6 NCBI Minute: The NCBI Application Programming Interfaces (APIs)


On September 6, 2017, we will present a webinar on Application Programming Interfaces (APIs) at NCBI.

Whether you’re new to APIs or are already using them, this webinar has something for you. We’ll introduce you to APIs and what they can be used for, then focus on the diverse group of APIs available to access NCBI databases and tools.

Date and time: Wed, Sep 6, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel.

You can learn about future webinars on the Webinars and Courses page.

GenBank release 221.0 is available via FTP, Entrez and BLAST


GenBank release 221.0 (8/13/2017) has 203,180,606 traditional records containing 240,343,378,258 base pairs of sequence data. In addition, there are 499,965,722 WGS records containing 2,242,294,609,510 base pairs of sequence data, 186,777,106 TSA records containing 167,045,663,417 base pairs of sequence data, and 1,628,475 TLS records containing 824,191,338 base pairs of sequence data.

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Yellow fever mosquito, 6 other organisms in July RefSeq genome annotations


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

  • Papio anubis (olive baboon)
  • Prunus avium (sweet cherry)
  • Aedes aegypti (yellow fever mosquito)
  • Chenopodium quinoa (quinoa)
  • Hevea brasiliensis (a eudicot)
  • Manihot esculenta (cassava)
  • Carlito syrichta (Philippine tarsier)
Portrait of olive baboon

Papio anubis (olive or anubis baboon)
Source: United States Fish and Wildlife Service: Digital Library System

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

August 30 NCBI Minute: NCBI Hackathons, a framework for rapid prototyping of pipelines for bioinformatics, biomedical informatics and genomics


NCBI regularly organizes hackathons throughout the United States, where participants work in teams to apply their data science experience with public datasets. In this NCBI Minute, you will hear highlights from recent hackathons, see examples of the software created in these events, and learn how you can participate in future hackathons.

Date and time: Wednesday, August 30, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

September 2017: NCBI to present EDirect workshop at NLM


On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.

NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.

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August 23 NCBI Minute: Using the Run Selector to Find Relevant Next-Generation Sequencing (NGS) Datasets


Do you have trouble searching the NCBI webpage for relevant datasets? Wish you could filter the search results more precisely? You can with SRA Run Selector.

In this NCBI Minute, you’ll learn how to filter the SRA database using the metadata details captured for each submitted dataset. This is easily done in a spreadsheet format that displays all recorded metadata for each SRA Run. The user-friendly interface allows you to selectively filter datasets down to the most relevant data for your research question and then export it in a spreadsheet.

Date and time: Wednesday, August 23, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI Replacing Obsolete NCBI Genomes (chromosome) and Removing Human ALU repeat elements (alu_repeats) BLAST databases


NCBI will discontinue both the NCBI Genomes (chromosome) and the Human ALU repeat elements (alu_repeats) BLAST databases in October 2017.

Better alternatives to NCBI Genomes (chromosome)

The existing NCBI Genomes (chromosome) database does not offer complete and non-redundant coverage of genome data. The newly added NCBI RefSeq Genomes Database (refseq_genomes) and the RefSeq Representative Genomes Database (refseq_representative_genomes) are more useful alternatives to the chromosome database. You can select these databases from the database pull-down list on any general BLAST form that searches a nucleotide database (blastn, tblastn).

nucleotide-nucleotide BLAST database menu

Figure 1. The nucleotide-nucleotide BLAST database menu with the recommended (RefSeq Genome and Representative genomes) and deprecated (NCBI genomes (chromosomes) and Human ALU repeats) databases highlighted.

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Sequence Viewer 3.22 now available


Sequence Viewer 3.22 has several new features, improvements and bug fixes, including improved rendering on BAM and cSRA tracks. For a full list of changes, see the Sequence Viewer release notes.

Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.