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Tag: Primer-BLAST
Apply to attend October 2022 interactive, hands-on workshops
Want to learn more about NCBI resources and how to implement our cutting-edge tools in your research? NCBI offers a variety of educational opportunities, including workshops, webinars, codeathons, tutorials, and more!
We are excited to announce our upcoming virtual workshop series for October 2022. Our interactive, hands-on workshops are taught by experienced NCBI Education Faculty. Applications are open to the public; however, each workshop will accept a limited number of participants to facilitate the best possible educational experience. Continue reading “New Upcoming NCBI Virtual Workshops!” →
Join us on June 2, 2021 at 12PM eastern time to learn how to how to upload and display your own genomic data in the context of annotated genome assemblies. You will use the Genome Data Viewer and the Sequence viewer to visualize your own uploaded data (indexed BAM, VCF, BED, wig, GFF formats), data from public track hubs, and your BLAST and Primer-BLAST results. You will also learn to take advantage of features of the viewers including optimizing display settings, sharing a view with collaborators, exporting images, and downloading genes or other features in the view.
- Date and time: Wed, June 2, 2021 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 theNCBI webinars playliston the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.
Missed our latest YouTube videos? Scroll down to see what we’ve been up to.
The National Institutes of Health encourages investigators to post preprints to public repositories in order to speed the dissemination and enhance the rigor of their work. This video demonstrates how to add preprint citations to My Bibliography.
Continue reading “NCBI on YouTube: Tips for My Bibliography, Genome Data Viewer and more” →
Join us on April 7, 2021 at 12PM eastern time to learn about new web BLAST and Primer-BLAST enhancements that improve your BLAST experience. You’ll also see a preview of some planned improvements to the databases that make it easier to find relevant matches.
Recent changes to web BLAST include added data columns on the descriptions table, so you can quickly find and sort your matches. Primer-BLAST now offers direct links from genome assembly pages, so you can easily select the specificity database. Primer-BLAST also now accepts multiple target templates making it easy to design primers that can amplify several similar sequences such as all splice variants of gene or the same target (16S, COI) from different strains or species.
- Date and time: Wed, April 7, 2021 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 theNCBI webinars playliston the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.
Do you work with data from organisms outside the traditional set of model organisms? Join us on March 10, 2021 to learn how to use NCBI resources including NCBI’s Taxonomy and BLAST that can help you find information from your organism and closely related taxa. You will see an example that shows you how to retrieve and download gene sequences for a set of species, generate multiple sequence alignments, and design primers using Primer-Blast.
- Date and time: Wed, March 10, 2021 12:00 PM – 12:45 PM EST
- 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 theNCBI YouTube channel. You can learn about future webinars on theWebinars and Courses page.
NCBI’s genome Assembly has a number of significant improvements!
Assembly records now have a link to Primer-BLAST making it easy to design primers in the context of a specific eukaryote genome assembly. Figure 1 shows the Assembly page for the Genome Reference Consortium Mouse Build 39 (GRCm39) with the link to Primer-BLAST.
Figure 1. The Assembly page for the mouse reference genome (GCF_000001635.27). Showing the new Run Primer-BLAST link, which loads the assembly as a database in the Primer-BLAST search (bottom) and the new expandable note sections, Genome-Annotation-Data in this case.
Continue reading “Improvements to NCBI Assembly” →
Primer-BLAST now has a “Primers common for a group of sequences” submission tab that allows you to design primers for a group of highly similar sequences. For example, you may want test for expression of any transcript of gene rather than a specific splice variant, so you want to design primers to cover all transcript variants. Or you may want to design primers that will amplify the same gene in closely related bacteria strains. To find primers for a group of related sequences, Primer-BLAST aligns the longest sequence to the rest to find common regions. It uses these to limit the locations of primers. The longest sequence is also used as the representative template sequence in the results. Figure 1 shows an example search for primers that will amplify all of the 15 splice variants for the human TP53 gene.
Figure 1. Primer-BLAST submission page and results for primers designed for the human TP53 transcripts. Top panel:The submission form with the “Primers common for a group of sequences” selected and the 15 RefSeq transcript accessions for TP53. Middle panel:The graphical results showing the longest sequence (NM_001126114.3) as the representative template, the locations of the primer pairs, and the alignment of the other template sequences. Bottom panel:An individual primer pair showing the locations on each of the template sequences.
Please try out this new feature and let us know what you think!
We’ve added a new feature (Max 3′ match), shown in Figure 1, to Primer-BLAST that limits the length of 3′ exon matches when designing exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in expression assays.
Figure 1. The new “Max 3′ match” option that limits the size of the 3′ match for exon-exon junction primers. This option helps avoid primers that may also produce product from genomic DNA. Continue reading “New feature added to Primer-BLAST to better design primers for expression assays” →
Primer-BLAST, NCBI’s primer-designer and specificity-checker, now offers a way to help you with irrelevant off-target matches.
Sometimes Primer-BLAST can’t design specific primers for your target sequence because of similar non-target sequences in the database. In some cases, you may know that these non-target matches are not important your research and are safe to ignore. Examples may include tissue-specific splice variants, redundant entries, and predicted sequences. To help in these cases, you can now choose to allow certain off-target matches. This gives Primer-BLAST greater freedom in primer selection and a better chance of finding highly specific primers.
Continue reading “Primer-BLAST now offers help with irrelevant off-target matches” →
We have made some recent improvements to the BLAST+ applications that take full advantage of the version 5 BLAST databases (BLASTDBv5), which include built in taxonomic information for sequences and no longer rely on the integer sequence identifiers (gi numbers).
With the latest version of BLAST, you can now:
Continue reading “Recent enhancements to BLAST+ (2.9.0): built-in taxonomy and access to proteins from the Pathogen Detection Project” →