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.
You’ve seen it before on shopping web site: you load a page displaying an item you want and see a list of other items that people bought with the one you’re viewing.
PubMed is free, but finding the important articles on a topic can cost a lot of time. To help you keep on top of the literature – with a little help from your fellow PubMed users – we are introducing a new type of link called “Articles frequently viewed together”. For some PubMed abstracts, you may see this link in the “Related Information” section in the right column.
Figure 1. The PubMed Also-Viewed feature.
BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the query, it treats all subject sequences the same, regardless of the quality of the sequence data or its annotation, and also does not allow easy comparisons between different subject sequences.
For example, the subject sequences may fall into multiple groups of similar sequences, or all of the subject sequences may be more similar to each other than to the query. A common way to obtain this information is to construct a multiple sequence alignment of the query and some or all of the subject sequences, but to this point, BLAST has not provided such alignments directly.
Enter SmartBLAST! SmartBLAST is a new and experimental NCBI tool that makes it easier to answer common sequence analysis tasks, such as finding a candidate protein name for a sequence, locating regions of high sequence conservation, or identifying regions covered by database sequences but missing from the query.
Welcome to PubMed Labs!
PubMed Labs is all about you. It’s a new NCBI initiative for creating innovative and relevant products by involving you, our user community, from the beginning.
PubMed Labs is about experimentation. It’s a place where you’ll find early versions of new tools, experimental content, and proposed features, as well as an opportunity to suggest ideas to us.
PubMed Labs is about learning. It’s a place where the focus is on figuring out what works, where failure is OK because it’s a learning experience, and where any idea is welcome that can improve our services for our users.
PubMed Labs is about conversation. It’s a place where we can share future plans with you, and you can tell us how we’re doing. It’s a place where we all can come together to create resources that will benefit the broader scientific community.
Join the conversation!
This blog post is geared toward genomics professionals.
From January 5th-7th, 2015, NCBI, in conjunction with the NIH Office of Data Science, held a genomics hackathon, where genomics professionals gathered to write useful, efficient pipelines for people new to genomics.
After we announced the hackathon, over 130 qualified applicants expressed interest in attending. Four team leads chose 23 attendees from this pool, then assigned initial predefined roles and provided biological guidance for a product in one of four subject areas: DNA-Seq, RNA-Seq, Epigenomics and Metagenomics. Continue reading