Category: Quick Tips

ClinVar annotations now available in NCBI Genome Browsers

Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer!

This track shows variation annotation, including single nucleotide variants and other short variants (e.g. insertions, deletions, etc.) in the NCBI ClinVar database and provides pathogenicity and other metadata. The ClinVar track is displayed next to the default NCBI and Ensembl gene annotation tracks and other NCBI-provided dbSNP and RNA-seq expression tracks.

screenshot of Genome Data Viewer with 'ClinVar variants' track displayed — **Figure 1.** GDV showing ‘ClinVar variants with precise endpoints’ track next to NCBI human gene annotation. Tracks are color coded for quick and easy interpretation. Legend is also provided.

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NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!

Introducing GaPTools for dbGaP Submitters

This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.

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NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets

It’s time we do another roundup of what’s been happening on YouTube!

First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more!

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Users of the SRA FTP site: Try the SRA Toolkit!

If you download data from the SRA (Sequence Read Archive) FTP site, we would encourage you to try the SRA Toolkit. This is particularly true if you use the SRA Fuse/FTP site at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant, which the SRA team will decommission on December 1, 2019.

The SRA Toolkit offers several advantages for downloading SRA data, including greater flexibility in specifying the data you need as well as access to public SRA data in the cloud. If you’re new to the Toolkit, you may want to start with these instructions.

If you have any questions or concerns about downloading SRA data, please contact sra@ncbi.nlm.nih.gov. We’d love to hear from you!

NCBI on YouTube: Request access to controlled data in dbGaP

Do you need access to controlled data in the database of Genotypes and Phenotypes (dbGaP)? This short video will show you how to request data today!

dbGaP archives and distributes the data and results from studies that have investigated the interaction of genotype and phenotype in humans. Responsible stewardship of controlled-access data subject to the NIH GDS Policy is shared among the NIH, the investigators approved to access the data, and the investigators’ institutions.

Easily configure gene feature modes in NCBI’s graphical sequence displays

Did you know you can easily switch between gene feature modes in NCBI’s graphical sequence displays like Sequence Viewer and GDV? You may need to configure gene tracks to suit your needs if, for example, you need to conduct analyses or present quality images.

Use one of two easy access points to the gene configuration menu to show the gene bar, the single line gene model or the expanded modes that show transcripts and CDSs.

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Change the way your graphs look with Genome Data Viewer’s enhanced settings

If you need to change your graph type – say, from histogram to line graph or a heat map – in Genome Data Viewer (GDV), you can now do so with a few clicks.

Click on the track name of any graph track to change the display (see Figure 1A, B and C).

Fig1 — Figure 1. Click on a track name to expose the graph settings menu (A). Set graph display style (B) to histogram, heat map or line graph (C).

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Hey Professors! Get your free personal assistant — an NCBI Account!

Professors, we know you’re busy — really, really busy. You have to develop and teach your courses and labs, coordinate and run your journal clubs and seminars, direct your lab’s research efforts, write grants and publications, counsel and mentor your students, and stay current on everything related to your teaching and research topics.

NCBI has information that can help with all of this, but there are so many interesting records and so little time to organize them. Sign up (Help) for or log in (Help) to your free NCBI Account and let us help you get started and get organized!

Read on – or watch the video embedded below – to learn more about what you can do with your NCBI Account.

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NCBI’s Genome Data Viewer now displays data from track hubs

The Genome Data Viewer’s (GDV) browser display now supports content provided in track hubs. This new GDV feature, summarized in this short video, extends the genome browser’s capability when it comes to viewing user-supplied data tracks alongside NCBI-provided tracks. You now have multiple options to analyze your data that include uploading your data (file/URL), streaming individual files from a remote location and/or connecting to a track hub. In all instances, GDV recognizes a variety of popular file formats with support for additional file formats planned. In the display, you can now also easily distinguish user-supplied tracks by their green-tinted track labels. Continue reading “NCBI’s Genome Data Viewer now displays data from track hubs” →

NCBI implements new, natural language sequence search

In late May, we introduced a new type of search experience in NCBI Labs that uses natural language queries to make common tasks easier. The experience at NCBI Labs – where we experiment with potential new features and tools – proved successful. We’re pleased to announce that we added this simplified search capability to NCBI’s global search page. Some natural language queries now work in the “All Databases” search from the NCBI home page!

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