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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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.
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.
Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.
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.
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.
We recently updated the BLAST AMI on Amazon Web Services (AWS). The AMI is preconfigured with BLAST+ 2.7.1 and supports a subset of the NCBI BLAST URL API. The latest version also addresses long download times and preservation of BLAST databases and results between reboots.
Useful Links:
You can now download human annotation release 109 on FTP or explore it in the Genome Data Viewer, in the Gene database, and with BLAST.
Highlights in release 109:
As you may have read in previous posts, NCBI is phasing out sequence GIs and transitioning to accession.version identifiers. To help you prepare for this transition, we created sample BLAST databases that will help you make code changes to your programs and workflows for the switch to accession identifiers.
The sample databases, env_nr_v5 and tsa_nr_v5, are on FTP.
If you have any questions or concerns, please contact our Help Desk.
Next Wednesday, April 11, 2018, at 12:00PM EDT, we will present a webinar that will help you enhance and expand your tabular saved BLAST results with basic Unix tools and the NCBI EDirect suite of programs. You will see how to add useful information to tabular format results like taxonomy, sequence titles, and links to sequence records and publications.
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.
The NCBI web BLAST service has many useful download formats, including the traditional pairwise output, tabular formats and highly structured formats. These formats allow you to easily save your BLAST results for later processing, editing and annotating.
The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.
