On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.
NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.
Do you have trouble searching the NCBI webpage for relevant datasets? Wish you could filter the search results more precisely? You can with SRA Run Selector.
In this NCBI Minute, you’ll learn how to filter the SRA database using the metadata details captured for each submitted dataset. This is easily done in a spreadsheet format that displays all recorded metadata for each SRA Run. The user-friendly interface allows you to selectively filter datasets down to the most relevant data for your research question and then export it in a spreadsheet.
Date and time: Wednesday, August 23, 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.
NCBI will discontinue both the NCBI Genomes (chromosome) and the Human ALU repeat elements (alu_repeats) BLAST databases in October 2017.
Better alternatives to NCBI Genomes (chromosome)
The existing NCBI Genomes (chromosome) database does not offer complete and non-redundant coverage of genome data. The newly added NCBI RefSeq Genomes Database (refseq_genomes) and the RefSeq Representative Genomes Database (refseq_representative_genomes) are more useful alternatives to the chromosome database. You can select these databases from the database pull-down list on any general BLAST form that searches a nucleotide database (blastn, tblastn).
Figure 1. The nucleotide-nucleotide BLAST database menu with the recommended (RefSeq Genome and Representative genomes) and deprecated (NCBI genomes (chromosomes) and Human ALU repeats) databases highlighted.
Sequence Viewer 3.22 has several new features, improvements and bug fixes, including improved rendering on BAM and cSRA tracks. 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.
Former NCBI Director Dr. David J. Lipman and the NCBI GenBank Team have been nominated for the Sammies People’s Choice Award. In addition to the People’s Choice Award, Dr. Lipman and the GenBank team, as well as the other nominees, are up for awards in seven categories; those winners will be selected by a committee of leaders in government, business, media, the non-profit community, and other areas.
The Sammies, known as the Oscars of government service, are a highly respected honor with a vigorous selection process. Named for the Partnership for Public Service’s late founder, Samuel J. Heyman, who was inspired by President Kennedy’s call to serve in 1963, these awards align with his vision of a dynamic and innovative federal workforce that meets the needs of the American people.
We are all invited to vote for the federal employees whom we think have made the most admirable contribution to the American people. The poll is open now at servicetoamericamedals.org/peoples-choice. Individuals are allowed to vote for multiple people/groups, up to once per day.
For the People’s Choice Award, organizers will be narrowing the field of finalists at several points, before announcing the winner at the Sammies gala on September 27th in Washington, DC.
Key dates to remember:
- August 1: Top 12 announced (out of first round of 26)
- September 1: Top 4 announced
- September 15: Voting closes
We congratulate Dr. Lipman, the GenBank team, and all the Sammies finalists.
The newest video on the NCBI YouTube channel shows you how to import sequences for alignment, run the MSA program, and display the results in Genome Workbench‘s multiple alignment view.
Subscribe to the NCBI YouTube channel to watch and receive alerts about new videos ranging from quick tips to full presentations.
From September 25-27,2017, NCBI will help with a bioinformatics hackathon at the University of Pittsburgh. The hackathon will focus on advanced bioinformatics analysis of next generation sequencing data, proteomics and metadata.
This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for bioinformatics analyses from high-throughput experiments. Some projects are available to non-scientific developers, mathematicians and librarians.
The event is open to anyone selected for the hackathon and willing to travel to the University of Pittsburgh (see below for venue address).
Have you ever searched the NCBI Protein database and been overwhelmed with the number of sequences returned? Have you tried searching with a protein name, thinking that would greatly limit the results, only to still be presented with many sequences (all with the same name)? It’s a common problem in this time of greatly expanding sequence databases powered by large-scale genomic sequencing of similar organisms. Redundancy in the sequence databases is high and only getting worse.
To address this, in 2013 NCBI released the WP records, which collect identical protein sequences annotated on bacterial genomes. In 2014, NCBI released the Identical Protein Reports on Protein records, which displays information about all other proteins identical to that protein. Now, we are releasing a new resource: Identical Protein Groups (IPG). IPG offers several features:
ClinVar, NCBI’s archive of submitted associations between alleles in the human genome and diseases or phenotypes, is now producing XML files that aggregate all submitted disease/phenotype information by variant (or set of variants) for public release via FTP bulk download. The new product, called ClinVarVariationRelease, is currently in beta release and will move to full release in early September 2017.
The newest video on the NCBI YouTube channel will show you how to have your PubMed searches automatically run and the results emailed to you daily, weekly or monthly. You will also learn how to create PubMed collections that you can share with others or keep privately for yourself.
Subscribe to the NCBI YouTube channel to receive alerts about new videos ranging from quick tips to full webinar presentations.