Join NCBI at PAG in San Diego, January 12–16, 2019


Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.

Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)

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BLAST+ 2.8.1 with New Databases and Better Performance


BLAST+ 2.8.1 is now available for download from our FTP site. This the first production release of standalone BLAST to support the new BLAST v5 databases (BLASTDBv5), which are also now available. The new databases have taxonomy information for the database sequences built-in.  This gives you the following important advantages over the v4 databases.

  1. The ability to limit your search by taxonomic group — species level as well as higher taxa.
  2. Improved performance when limiting BLAST search with accessions.
  3. Retrieval of sequences by taxonomic group from a BLAST database with blastdbcmd.

There are some additional enhancements to the search program options.

  1. A new option (-subject_besthit) culls HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP. This is an experimental option and is subject to change.
  2. Use of the -max_target_seqs option for formats 0-4 is now allowed. The number of alignments and descriptions will be set to the max_target_seqs.
  3.  BLAST now issues a warning  about the possibility not seeing all equivalent matches if -max_target_seqs is set to less than five.

The new release also includes a few bug fixes.  Please see the release notes for additional details and, as always, write to us at blast-help@ncbi.nlm.nih.gov with any questions.

Visit NCBI at the ASCB | EMBO meeting in San Diego, December 9-11, 2018


Going to the ASCB | EMBO meeting? Stop by the NCBI booth (#327) to learn about all that NCBI has to offer, ask questions, and provide feedback on how we can better meet your needs for research and teaching.

Booth #327, Exhibit Hall:

  • Sunday, December 9, 9:30 AM – 4:00 PM
  • Monday, December 10, 9:30 AM – 4:00 PM
  • Tuesday, December 11, 9:30 AM – 4:00 PM

Visit the booth anytime during exhibit hours to discuss any topic or just to say hello. We’re also offering specific times at the booth for focused conversations about using specific sets of NCBI resources in your research and teaching.

Discussion Sessions:

Sunday

  • 12:30 PM  NCBI BLAST in research and teaching 

Monday

  • 12:30 PM   Jupyter notebooks to teach scripting and NCBI resources

Tuesday

  • 12:30 PM    EDirect  for command-line access  to NCBI databases
  • 2:00 PM    Jupyter notebooks to teach scripting and NCBI resources

To stay up-to-date about NCBI at ASCB or in general, follow us on Twitter at @NCBI ‏.

 

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

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Update: NCBI is now in the process of merging EST and GSS records into the Nucleotide database, and we expect to complete this process in early 2019. Accession.version and GI identifiers will not change during this process.

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.