Sequence Viewer 3.23 has several new features, improvements and bug fixes, including performance optimization for alignment renderings and improved tooltips in uploaded VCF files. 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.
Copy number variants (CNVs) from ExAC’s publication are now available at dbVar as nstd151. The data include approximately 50,000 CNV regions identified from 60,000 human exomes, providing a deep survey of common and rare copy number variation affecting protein-coding sequences in the human genome.
dbVar provides FTP files in VCF, GVF, and CSV formats, and include placements on GRCh37 as well as remapped placements on GRCh38. Tutorials for working with different formats are also available.
Follow the dbVar RSS feed for information on monthly releases.
We recently updated the HIV-1 interaction datasets in Gene with data provided by the Southern Research Institute (SRI).
The protein interactions dataset now has:
The replication interactions dataset now has:
Data are also available at the RefSeq HIV-1 website and the GeneRIF FTP site.
NLM needs your input. We are experimenting with a new PubMed search algorithm, as well as a modern, mobile-first user interface, and want to know what you think. You can try out these experimental elements at PubMed Labs, a website we created for the very purpose of giving potential new PubMed features a test drive and gathering user opinions.
Please note that PubMed Labs includes only a limited set of features at this time and not the full set of PubMed tools. The absence of a feature or tool on PubMed Labs does not mean we plan to eliminate it from PubMed; it simply means we are not testing it now!
The key elements we are testing are:
Based on analysis of data obtained from anonymous PubMed search logs, we have developed a new algorithm that we believe does a much better job of sorting search results by their relevance, or “best match,” to your query. This new algorithm incorporates machine learning to re-rank the top articles returned.
We were so excited by results with this algorithm that we already implemented it in PubMed, but it is still experimental and we would very much appreciate hearing what you think. Part of our test in PubMed Labs is having best match be the default sort, instead of PubMed’s default of sorting by most recent articles. If you find that you prefer to sort by the most recent articles instead, it takes only a simple click of a button to do so.
Interested in specifics about the new algorithm? You can read more in this NLM Technical Bulletin.
Genome-wide association studies (GWAS) usually rely on the assumption that different samples aren’t from closely related individuals. If you’re using combined datasets that have been genotyped on different platforms, though, how do you detect duplicates and close relatives?
The dbGaP team at NCBI developed a new software tool and rapid statistical method called Genetic Relationship and Fingerprinting (GRAF) to do exactly that. At NCBI, we use GRAF as a quality assurance tool in dbGaP data processing. We’re presenting this tool publicly so any researcher can check the quality of their own data.
GRAF uses two statistical metrics to determine subject relationships directly from the observed genotypes, without estimating probabilities of identity by descent (IBD), or kinship coefficients, and compares the predicted relationships with those reported in the pedigree files. Please see the PLOS ONE article published in July 2017 for a detailed description of GRAF.
A recent update to GRAF adds the ability to determine subject ancestries. For more information on this addition, visit Poster #1322T, “Quickly determining subject ancestries in large datasets using genotypes of dbGaP fingerprint SNPs”, on Thursday, October 19th from 3-4 in the Exhibit Hall at ASHG.
Recent updates to Genome Workbench include a new navigation tutorial for Graphical Sequence View, and various bug fixes and improvements. You can see the full list of changes in the Genome Workbench release notes.
Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse data in GenBank and combine this data with your own private data.
About two years ago, NCBI launched PubMed Labs, a gathering place for discovering and experimenting with new features and content for NCBI’s family of websites. Over those years, we launched a few experiments that have helped us learn more about our customers and how we can serve them better.
Today we’re happy to announce that we’re expanding PubMed Labs to a broader set of experiments called NCBI Labs.
This blog’s menu item and blog category “PubMed Labs” will now appear as “NCBI Labs”. Existing links will continue to work. We won’t be updating the old blog posts, for the most part, although some links on existing sites (e.g. on PubMed Journals) may be updated to use the new name.
On October 11, 2017, NCBI will present a webinar on RefSeq Functional Elements. This NCBI Minute will introduce you to this project and its scope, describe how functional elements are curated and displayed, demonstrate how to access the data, and provide information on the current progress of the project.
Date and time: Wed, Oct 11, 2017 12:00 PM – 12:30 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
The new RefSeq Functional Elements project is an expansion of the NCBI RefSeq project to include non-genic functional genomic regions in human and mouse that have been experimentally validated and described in the scientific literature.
On October 4, 2017, NCBI staff will present a webinar on author disambiguation and the advantages of using an ORCID ID.
Disambiguating common author names is tough in any field, but if your published research is cited in PubMed, we can help you find your citations, create a bibliography, and share your publication list with others.
In this webinar, we’ll also talk about the advantage of quickly registering for a free, unique identifier that will remain constant – even if your name changes.
Date & time: Wednesday, October 4, 2017 12:00 PM – 12:30 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
The newest version of Magic-BLAST (v. 1.3.0) offers improved sensitivity and faster run-times as well as a number of other new features and improvements. These include the ability to set the alignment cut-off score as a function of read length, a maximum edit distance option and optional local cacheing for SRA files. For more information on these and other improvements, see the release notes. You can download the new executables from the NCBI FTP site.
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more here.
