NLM In Focus blog profiles Dr. Kim Pruitt, NCBI Staff Scientist

The inaugural article in NLM In Focus’s new series on NLM scientists features Kim Pruitt, PhD. Dr. Pruitt is a staff scientist at NCBI; she heads the Reference Sequence Database, better known as RefSeq.

In the article, Dr. Pruitt shares her career trajectory as well as pearls of wisdom for young scientists.

Click through to read NLM's profile on Kim Pruitt, PhD.

Click on the picture to read NLM’s profile on Kim Pruitt, PhD.

Introducing Magic-BLAST

Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site.

Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-Seq, locating the candidate introns and adding up the score of all exons. Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files.

Magic-BLAST implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries. Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis. Read more about Magic BLAST on the FTP site.

NCBI’s Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database

On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information’s PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting & Exposition in Philadelphia.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

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Second Round of HTTPS Tests

NCBI has scheduled the next round of HTTPS tests, following up from the initial tests performed on September 15.

The schedule for these tests is as follows (all times are EDT):

Thursday, Sept 22
8:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS, same as the first test on Sept 15.
8:00 AM – 9:00 AM : redirect CGI’s and API calls to HTTPS where possible, reject where not possible

Monday, Sept 26
8:00 AM – 10:00 AM : redirect web pages from HTTP to HTTPS with HSTS activated using a 1-hour expiration
10:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS without HSTS

Tuesday, Sept 27
8:00 AM : Start continually redirecting web pages from HTTP to HTTPS

If you use NCBI APIs, please see

For more detailed information about these tests, please see

Important considerations:

  • If you develop software that depends on NCBI APIs or toolkits (e.g. SRA or C++), please target the 8-9 AM window on Sept 22 for testing, as we expect any problems with HTTPS to result in failures of affected applications during this test.
  • Some browsers may cache the HTTPS pages viewed during the test periods, and so may continue to request pages over HTTPS once the tests are complete. If this causes problems, clearing the browser’s cache and cookies will restore access over HTTP.
  • We will be running additional tests on CGI applications once we analyze the results of the tests on September 22.

NCBI Begins HTTPS Tests

You may have heard that NCBI, along with the rest of the Federal Government, is switching to HTTPS-only access. To help prepare for this, NCBI is beginning a series of tests. During these tests, all traffic to NCBI will be redirected from HTTP to HTTPS to simulate our system’s behavior once the HTTPS transition is complete.

The first test will be Thursday, September 15, from 8:00-9:00 AM EDT.

If you experience problems with any NCBI site or service during that hour, please see our Secure Website Tests plan for advice on how to proceed.

If you use software that accesses NCBI data, and you experience problems with that software, we recommend that you contact the software vendor, as they may need to update their products to work over HTTPS.

If you use proxies to access NCBI (for example, EZProxy) and you experience problems during this period, we also recommend that you contact the proxy service to ensure that your service is ready for HTTPS.

If you develop software that accesses NCBI services or that depends on NCBI APIs (such as the E-utilities) or toolkits (such as the SRA or C++ toolkits), these tests are a great opportunity for you to see how your software will function over HTTPS.

If you have other questions or concerns, please contact us at

The Future of Existing GI Numbers at NCBI

NCBI has announced that we will be changing the way we handle GI numbers for sequence records in September 2016. (Read more, in case you missed it).

In this post, we’ll address a key question:

What is the future of existing GI numbers?

The short answer is that nothing is happening to these GI numbers.

If a nucleotide or protein record already has a GI, it will continue to have that GI indefinitely. You will also be able to retrieve such a record using its GI either on the NCBI web site or using the E-utilities.

Moreover, GIs will remain part of the XML and ASN.1 formats of sequence records.

If not GIs, then what?

Accession.version identifiers. All sequence records, both new and old, will have a unique accession.version identifier.

Existing records will keep the accessions they already have; new sequences will only receive an accession.version identifier.

So what’s all the fuss about?

Two things:

Stay tuned for additional posts about this topic, and please contact us if you have questions.

Find, Browse and Follow Biomedical Literature with PubMed Journals

Following the latest biomedical literature can be a challenge, but NCBI’s new PubMed Journals will help you keep up-to-date.

PubMed Journals lets you:

  • Easily find and follow journals of interest
  • Browse new articles in your favorite journals
  • Keep up-to-date with a Journal News Feed containing new arrivals, news links, trending articles, and important article updates (retractions and more!)

The PubMed Journals home page.

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NCBI is Phasing Out Sequence GIs – Here’s What You Need to Know

You may have heard that NCBI is changing the way we handle GI numbers for sequence records in September 2016. Well, you heard right! Here’s the announcement, in case you missed it.

There are a number of issues raised by these changes, but we’re going to answer two questions in this post:

  1. What pieces of your code will break in September?
  2. Are GI numbers gone for good?

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Fast Sequence Inspection with ORFfinder + SmartBLAST

intro pic

This blog post is intended for all BLAST users.

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

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Streptococcus pyogenes “A to Zs” Covered in New Book, Freely Available on NCBI Bookshelf

The University of Oklahoma Health Sciences Center has published an open-access book called “Streptococcus pyogenes: Basic Biology to Clinical Manifestations” that provides a comprehensive review of research on the bacteria. The university’s first online, open-access book, “Streptococcus pyogenes” is freely available on NCBI’s Bookshelf, at
S.pyogenes Book on the NCBI Bookshelf

Streptococcus pyogenes (Group A Streptococcus) is responsible for diseases such as scarlet fever, pharyngitis, impetigo, cellulitis, necrotizing fasciitis and toxic shock syndrome, as well as the sequelae of rheumatic fever and acute poststreptococcal glomerulonephritis. The book aims to provide an up-to-date and comprehensive review of research on Streptococcus pyogenes, including its basic biology, epidemiology, genetics and pathways that facilitate group A streptococcal infections. Continue reading