Author Archives: NCBI Staff

About NCBI Staff

The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.

NCBI to help with Rocky Mountain Genomics HackCon at University of Colorado BioFrontiers Institute June 18 – 23, 2018

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The NCBI will assist with a plenary session and a hackathon at the BioFrontiers Institute in Boulder Colorado June 18-23rd.

The hackathon will focus on tools for advanced analysis of biomedical datasets including text, images, next generation sequencing data, proteomics, and metadata. Many individuals who attend these events have already engaged in the use of large datasets or in the development of informatics tools, code, or pipelines; however, researchers who are in the earlier stages of their data science journey, including students and postdocs are also encouraged to apply. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to Boulder, Colorado.

Before the hackathon, there will be a one-day Plenary Session, featuring technical speakers in precision medicine, metagenomics and advanced RNA-Seq analysis, as well as an exhibitor and poster session.  Please see https://hackathon.colorado.edu for more details.

There will also be an advanced nascent RNA-Seq workshop, as well as an advanced pipelining workshop, run solely by the University of Colorado, although NCBI personnel may be present.  Please see https://hackathon.colorado.edu for more details.

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Testing Periods for New API Keys

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You’ll want to pay attention to this if you regularly use the E-utilities API. As we announced last fall, we are in the process of introducing API keys for the E-utilities. This post will update the schedule of this process and outline our release plan, which will include a series of testing periods.

So what’s happening?

We’re learning a lot from you!

Thanks for all of your feedback! Ongoing conversations with our users are helping us plan this release in a way that will benefit everyone as much as possible. Please continue to reach out to us with ideas and suggestions!

The effective date for release of API keys has been pushed back.

We will not be activating API keys on May 1, 2018 as originally announced. That date is being moved to be no earlier than September 1, 2018.

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April 25 NCBI Minute: Revised Release Plan for the New NCBI API Keys

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As previously announced, NCBI is introducing API keys for the E-utilities. This NCBI Minute will review these keys and their benefits for API users, and will update the schedule for when we will activate these keys. We will also describe plans for a test site and a series of testing periods during which these keys will be fully active. These periods are an ideal opportunity for developers to test their products in this new environment.

Please register and join us for this webinar to be presented on Wednesday, April 25, 2018 at noon, Eastern time.

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.

BLAST is transitioning to accession.version-based databases

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As you may have read in previous posts, NCBI is phasing out sequence GIs and transitioning to accession.version identifiers.  To help you prepare for this transition, we created sample BLAST databases that will help you make code changes to your programs and workflows for the switch to accession identifiers.

The sample databases, env_nr_v5 and tsa_nr_v5, are on FTP.

If you have any questions or concerns, please contact our Help Desk.

April 11 webinar: Getting the most out of web BLAST tabular format

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Next Wednesday, April 11, 2018, at 12:00PM EDT, we will present a webinar that will help you enhance and expand your tabular saved BLAST results with basic Unix tools and the NCBI EDirect suite of programs. You will see how to add useful information to tabular format results like taxonomy, sequence titles, and links to sequence records and publications.

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.

The NCBI web BLAST service has many useful download formats, including the traditional pairwise output, tabular formats and highly structured formats. These formats allow you to easily save your BLAST results for later processing, editing and annotating.

BLAST+ database improved

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We’ve made some recent enhancements to the BLAST+ applications that allow you to:

  1. Limit your search by taxonomy using information built into the BLAST databases
  2. Search sequences by accession faster
  3. Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database

The new version of the BLAST databases (version 5, release notes) supports the items listed above. You can access the new executables on FTP. Sample version 5 databases are also available.

Note: This is an alpha release to allow users to test and comment on new features.

Problems/Feedback

Please send problem reports and feedback to blast-help@ncbi.nlm.nih.gov or write to the Help Desk.

Sequence Viewer 3.25 now available

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Sequence Viewer 3.25 has several new features, improvements and bug fixes, including a new user interface and programmatic API to attach and show HTTP based BAM files, as well as improved usability of zoom functions and tooltips for RNA features. 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.

RefSeq release 87 available

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RefSeq release 87 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript and protein data available as of March 5, 2018 and contains 155,118,991 records, including 106,245,682 proteins, 21,923,574 RNAs, and sequences from 77,225 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings.

Starting in July 2018, SNP variation features will no longer be in RefSeq genome assembly records – chromosome and contig records with NC_, NT_, NW_ and AC_ accession prefixes.  The RefSeq release notes have more information about this change.

See your data in context with NCBI’s updated Genome Data Viewer

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We know it’s important to you to be able to browse and visually inspect variants and alignments from your next-gen sequencing experiments, so we’ve added remote streaming of BAM files to the Genome Data Viewer (GDV). All you need are your BAM files and the index files (.bai extension) in a location that allows HTTP access and you can stream BAM files as custom tracks into the GDV.

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GenBank exceeds 3 Terabases in release 224

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GenBank release 224.0 (2/13/2018) has 207,040,555 traditional records (including non-bulk-oriented TSA) containing 253,630,708,098 base pairs of sequence data.

In addition, there are 564,286,852 WGS records containing 2,608,532,210,351 base pairs of sequence data, 214,324,264 TSA records containing 193,940,551,226 base pairs of sequence data, and 12,819,978 TLS records containing 4,531,966,831 base pairs of sequence data.

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