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 http://www.ncbi.nlm.nih.gov/books/NBK333424/.
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

Professors:  NCBI can help you streamline your teaching and research efforts


Professors, you’re busy – really busy. You have to develop and teach your courses and laboratory sessions, coordinate your lab’s research efforts, write grants and publications, and stay current on everything related to your teaching and research topics.

NCBI has information that would help most of these efforts – but there are so many interesting records and so little time to organize them for efficient use. Sign up for a free NCBI Account and let us help you organize your important lists!

my ncbi login page

Figure 1. The My NCBI login page.

Sign up for an NCBI Account – or sign in to your account if you already have one – and:

  • Store and automate your searches;
  • Save and manage collections of important records for use in coursework, research projects and federal grants;
  • Create public lists for students in your courses and your own Faculty Profile;
  • And keep track of everything – right on your My NCBI dashboard.

Read on to find out how to do all of these things and more!

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Researchers identify potential alternative to CRISPR-Cas genome editing tools


An international team of CRISPR-Cas researchers has identified three new naturally-occurring systems that show potential for genome editing. The discovery and characterization of these systems is expected to further expand the genome editing toolbox, opening new avenues for biomedical research. The research, published October 22nd in the journal Molecular Cell, was supported in part by the National Institutes of Health.

“This work shows a path to discovery of novel CRISPR-Cas systems with diverse properties, which are demonstrated here in direct experiments,” said Eugene Koonin, Ph.D., senior investigator at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), part of the NIH. “The most remarkable aspect of the story is how evolution has achieved a broad repertoire of biological activities, a feat we can take advantage of for new genome manipulation tools.”

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The NCBI Minute: quick introductions to NCBI resources


For over two years, NCBI has presented webinars on a wide range of topics to a growing audience. More recently, we began offering shorter webinars in a series called The NCBI Minute.

These presentations introduce a new NCBI tool or resource or provide quick tips for using a popular resource in 5-10 minutes.

screenshot of popular NCBI Minute presentations on YouTube

Figure 1. Examples of popular NCBI Minute presentations; SmartBLAST Introduction presented September 2 (YouTube), and Connecting with PubMed Commons presented May 2 (YouTube).

Each NCBI Minute is recorded and posted on our YouTube channel in the NCBI Minute playlist. Two of our most popular NCBI Minute presentations (Figure 1) are the introduction to the new SmartBLAST service, first described on NCBI Insights in July, and Connecting with PubMed Commons, our public commenting service for PubMed articles described in several NCBI Insights posts.

Missed a presentation? No problem!

If you missed any of The NCBI Minute, there are two ways you can catch up:

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SRA Toolkit: the SRA database at your fingertips


The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems.

Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.

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Fine-tune your web-based search results with SRA Run Selector


Run Selector is a tool available through the Sequence Read Archive (SRA) that allows you to fine-tune your web-based search results. There are over two dozen fields that can be used to filter SRA data in Run Selector. For example, if you need to look at data from a particular sequencing platform and genome assembly, you can use these fields as filters.

After running a web-based search for any keyword in the SRA database, users can dump all the results (up to a maximum of 20,000 experiments) into the Run Selector for fine-tuning. In addition, Run Selector shows you how many runs fall into each of the categories even before a filtering category is selected, allowing you to investigate the data further by noting what is contained within the database.

post 2 fig 1 run results

Figure 1. After searching with SRA, click on “Send to” to open the drop-down menu. Then click on the radio button labeled “Run Selector” to send your search results to Run Selector. Note that you can already see how many runs are in each of the categories to the left.

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Troubleshooting GenBank Submissions: Annotating the Coding Region (CDS)


This article is intended for GenBank data submitters with a basic knowledge of BLAST who submit sequence data from protein-coding genes.

One of the most common problems when submitting DNA or RNA sequence data from protein-coding genes to GenBank is failing to add information about the coding region (often abbreviated as CDS) or incorrectly defining the CDS. Incomplete or incorrect CDS information will prevent you from having accession numbers assigned to your submission data set, but there is a procedure that will help you troubleshoot any problems with the CDS feature annotation: doing a BLAST analysis with your sequences before you submit your data.

Here’s how to use nucleotide BLAST (blastn) and the formatting options menu to analyze, interpret and troubleshoot your submissions:

1. To start the BLAST analysis, go to the BLAST homepage and select “nucleotide blast”.

nucleotide blast link. click to start BLAST analysis

Figure 1. Select “nucleotide blast”.

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Finding Chemical Probes and Modulators – The Hunt for New Chemical Reagents and Medicines


This blog post is a continuation of last week’s blog on finding biological assay data; it is intended for researchers who use PubChem.

Your research focuses on a protein (receptor or enzyme) for which you’d like to identify a chemical probe or modulator. The probe could help to identify the subcellular location of a protein. A modulator may help to determine the biological effects of a particular protein’s activity. Additionally, finding a novel chemical that binds to your protein might assist you in exploring the use of a new class of therapeutics in drug design.

At NCBI, the PubChem BioAssay database stores biological activity assay information, which makes it possible to find experimentally measured targets for millions of chemicals. This blog post shows a simple workflow to download a table (with raw and kinetic data) of chemicals that have been determined to bind to a particular gene/protein target.

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