October 3, 2018 Webinar: Using BLAST Well


Next Wednesday, October 3, 2018, the lead of the NCBI BLAST group will show you how to be more effective with NCBI’s standalone BLAST applications. You will learn how to optimize database selection, output formats, taxonomy information and use our next-gen alignment program Magic-BLAST.  You can also use many of these strategies to improve your web BLAST searches.

Date and time: Wed, Oct 3, 2018 12:00 PM – 12:45 PM EDT

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.

Magic-BLAST (v1.4.0), an accurate DNA and RNA-Seq aligner


What is Magic-BLAST and why are we excited about it?

Magic-BLAST is a BLAST tool, but it’s unlike any other.

It aligns next generation sequencing reads, both DNA and RNA-seq.  It implements the aligner algorithm from MAGIC [1], a trusted pipeline, but uses the well tested and supported BLAST infrastructure. We think it’s like putting two great things together, like having your favorite ice cream in your morning coffee.

We’re so excited about it that we even wrote an article that compares Magic-BLAST to a few other aligners on several data sets.

If you look at the figures in our article, we think you’ll see that Magic-BLAST excels at finding introns and processing ultra-long sequences. It also can handle high levels of mismatches as well compositionally biased DNA.  Finally, you’ll see that Magic-BLAST works in a lot of relevant situations in which current aligners won’t. If our results got your attention, here is our documentation, which includes a cookbook with a few examples.

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Upcoming Changes to EST and GSS Databases


As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database. This change will provide a single point of access for all GenBank sequence data with a common look and feel.

Read more to learn about how this change affects these resources:

  • Websites (Entrez)
  • APIs (E-utilities)
  • FTP sites
  • Submission procedures
  • BLAST
  • TSA (have a look if you’re not familiar!)

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July 25 NCBI Minute: Five Teaching Examples Using NCBI BLAST


Next Wednesday, July 25, 2018, NCBI staff will show you a set of simple teaching examples that use BLAST and related alignment tools at NCBI to explore modern biology concepts and techniques including evolution, taxonomy, homology, multiple sequence alignment, phylogenetic trees, primer design and gene expression analysis. You can easily incorporate these examples into your undergraduate biology courses.

Date and time: Wed, July 25, 2018 12:00 PM – 12:30 PM EDT

Register here.

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 our Webinars and Courses page.

The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)


Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV to execute and manage BLAST queries (blastn, tblastn) aligned to the specific assembly displayed in GDV.

To learn about this tool, keep reading or watch this short introduction video. Further details are in GDV’s help documents.

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5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more


Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

NCBI Minute: Getting the Most out of Web BLAST Tabular Format

The NCBI web BLAST service has several useful download formats, including tabular formats. All formats allow you to easily save your BLAST results for processing, editing, and annotating.

This video will show you how to use basic Unix tools and EDirect to expand and enhance your tabular saved BLAST results. You will also see learn how to add useful information like taxonomy and sequence titles.

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


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.

Tour the NCBI’s Genome Data Viewer, Bookshelf, Pathogen Isolates Detection Browser and other resources on YouTube


Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.

NCBI’s Genome Data Viewer – Introducing the BLAST Widget

A brief introduction into how the BLAST widget, a new addition to the Genome Data Viewer, helps you see your BLAST results in the context of assembled genome sequences.

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May 16 webinar: Improved Standalone BLAST database and programs: now with taxonomic information


Next Wednesday, May 16, 2018, we’ll show you how to download and use the latest standalone BLAST databases, dbv5. You’ll learn how to use BLASTdbv5 and the new BLAST programs to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy.

Date and time: Wed, May 16, 2018 12:00 PM – 12:30 PM EDT

Register here: https://bit.ly/2qW7LLy

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.