IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin and T cell receptor variable domain sequences. We’ve released a new version of IgBLAST with three new improvements:
The new release determines the V gene reading frame from the end of FWR3 region instead of end of V gene. This helps identify the correct reading frames for rearrangements that have insertions or deletions near the V gene end.
The allowed distance between V gene end and J gene start has been increased to 225 bp to allow detection of ultra long D/N regions.
The standalone program and files has been repackaged to make it easier to install.
The new release is available from the BLAST FTP area, along with a new manual on GitHub.
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.
The ability to limit your search by taxonomic group — species level as well as higher taxa.
Improved performance when limiting BLAST search with accessions.
Retrieval of sequences by taxonomic group from a BLAST database with blastdbcmd.
There are some additional enhancements to the search program options.
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.
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.
BLAST now issues a warning about the possibility not seeing all equivalent matches if -max_target_seqs is set to less than five.
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.
12:30 PM NCBI BLAST in research and teaching
12:30 PM Jupyter notebooks to teach scripting and NCBI resources
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 .
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
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.
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 , 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.
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:
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
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.
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.