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 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 https://go.usa.gov/xKf8H
For more detailed information about these tests, please see https://go.usa.gov/xKH6Y
- 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.
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 firstname.lastname@example.org.
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?
Stay tuned for additional posts about this topic, and please contact us if you have questions.
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.
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/.
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
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.”
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.
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:
This blog post is directed toward medical or science librarians in the United States who offer bioinformatics education and support services or are planning to offer such services in the future.
The NCBI, in partnership with the National Library of Medicine Training Center (NTC), will once again offer the Librarian’s Guide to NCBI course on the NIH campus, March 7-11, 2016 (Announcement). This will be the fourth presentation of the course, and there are now 69 graduates of the training program.
These graduates represent 61 libraries, hospitals and government agencies from 27 states and the District of Columbia. Librarian’s Guide graduates now form a core community of NCBI-trained bioinformatics support specialists who maintain collaboration and mutual support through an online forum and monthly NCBI “Office hours” videoconference discussion sessions with course faculty and students. Materials from the 2013, 2014 and 2015 courses are available now, as well as lecture videos for the expression module.
Figure 1. Participants in the March 2015 A Librarian’s Guide to NCBI course. This class included 29 biomedical and science librarians.
This blog post is geared toward researchers.
In November, NIH announced a new format for biographical sketches (biosketches); the new format is required for grant applications submitted for due dates after May 24, 2015 (see NOT-OD-15-032). SciENcv, a tool available through My NCBI for creating biosketches, has been updated to reflect the format changes and to help users convert their existing NIH biosketches from the old format to the new.
What changed with the NIH Biosketch?
Differences between the old and new NIH Biosketch formats include:
- Maximum length increased from 4 to 5 pages
- Rearranged data in the table at the top of the Biosketch
- Section A, Personal Statement can now include up to 4 supporting citations
- Section C is now called “Contribution to Science” and should be comprised of up to 5 brief descriptions of your most significant contributions to science, each with up to 4 supporting citations. In addition, you may also provide a URL to a full list of your published work as found in a publicly available digital database such as My Bibliography. This section is the most notable difference in the new format.