Category Archives: Quick Tips

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

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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

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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

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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

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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!

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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

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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 implements new, natural language sequence search

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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!

NCBI search bar, red arrow pointing to all databases

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June 20 NCBI Minute: Getting the Genomic Context for BLAST Protein Matches

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Do you ever want to see the flanking genes of a protein match from a BLAST search?  On June 20th, we’ll show you how to see the genomic context of bacterial proteins using the identical protein report and the graphical sequence viewer. You will also learn to use these reports in detail and how to get these genomic contexts in batch for a set of protein matches using the identical proteins report and EDirect .

Date and time: Wed, June 20, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

February 14th NCBI Minute: How to quickly retrieve a sequence from NCBI

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On Wednesday, February 14, 2018, NCBI will present a webinar that will show you how to quickly retrieve sequences in any format from NCBI.

Date & time: Wed, Feb 14, 2018 12:00 PM – 12:30 PM EST

Ever need to quickly grab a protein or nucleotide sequence in FASTA or another format from NCBI? This NCBI Minute will show you how to accomplish this using the nucleotide and protein web pages, an NCBI URL, and – the most flexible way – through the commandline EDirect client that accesses the E-Utilities API.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.