Tag Archives: Primer3

View External Tools

Video Tip of the Week: Send UCSC Genome Browser sequence to external tools

The folks at the UCSC Genome Browser are always adding new features, new data, and new genomes to their site. And although they use the genome-announce mailing list to get the word out, even I can miss a notice. There was news recently of a new feature associated with the graphical genome browser that I’ve been waiting for (as I had tested it prior to roll-out), but they sent the email out when I was prepping for Thanksgiving, and I didn’t catch it for a few days.

But now I’ve had a chance to see it, kick the tires more, and I want to show you how it works. The basic feature is this: you can take the genomic sequence from the window you are viewing and with a couple of clicks deliver it right to another tool for more helpful data or analysis. This is really handy from the graphical viewer. Before you were limited to obtaining the sequence with the “Get DNA” option. You could get the sequence, copy/paste, and do whatever. Which is fine, and might still be right for some other tools. But now you can skip that copy/paste part and explore features of your sequence directly. If you don’t have time for the video, here’s the bullet–use this View–>In External Tools menu to get there.

View External Tools

There are a range of options. You can still jump right to NCBI Map Viewer or Ensembl to look at the same region in their browsers. But now you can select primers, see restriction sites, look at RNA characteristics, find protein domains, or examine CRISPR tools. You can look for transcription start sites or some TF binding motifs. Here’s this week’s Video Tip that shows the process.

You can still “get DNA” if you want to. And you can still use the Table Browser to send data from your custom queries to even more tools (like Galaxy and others). But we know from our workshops that most people we train spend their time in the graphic browser and these tools should help them accomplish more. You can see all of these options in our freely available training suites (linked below).

To see if there are other things you missed over the past year, check out the new NAR database issue paper from the UCSC team (linked below). It has updates about many of their accomplishments and recent features, so have a look and see if there are other useful aspects for assisting your research.

Quick links:

UCSC Genome Browser: http://genome.ucsc.edu/

Intro full training suite: http://openhelix.com/ucsc

Advanced topics training suite: http://openhelix.com/ucscadv


Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, W. (2015). The UCSC Genome Browser database: 2016 update Nucleic Acids Research DOI: 10.1093/nar/gkv1275

Disclosure: UCSC Genome Browser tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.

Simple primer design tools on the web

ResearchBlogging.orgThere are a lot of really complex bioinformatics tools and databases out there. But so often in training situations people ask us for something that solves a problem that is rather small and simple by comparison to genotype frequencies in the human populations. Sometimes they just need primers for their experiments.

I know there are commercial tools out there, and if you have a favorite you can let us know in the comments. But one very simple and free tool that people can use for primer design is Primer3. We have had a tutorial in our subscription collection about Primer3 for a long time since people asked us so frequently for this.

You can often find the software for Primer3 integrated in analysis pipelines too. If you do a primer search with the in silico PCR tool on the UCSC Genome Browser you will get some Primer3 features output. And another group decided to create a tabbed interface for Primer3 to increase usability and make it a bit less daunting–Primer3Plus. But I always sort of liked the basic interface, because I could see all my options at once. However, I can see that the tabs make sense for some people.

The Primer3Plus team described their work in a paper in NAR. Their goals were to make it a bit less daunting for occasional users, but still keep the features that more advanced users need available. So instead of one long page, the pieces of Primer3 were tabbed: General Settings, Advanced Settings, Internal Oligo, Penalty Weights and Sequence Quality. They designed the features around the user scenarios of Detection, Cloning, Sequencing, Primer Checking, and Lists of primers. Their documentation explains their thoughts and the software functions around these as well.

Primer3 is a real workhorse for everyday tasks. And freely available to use or download–with appropriate citations, of course!

Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386 DOI: 10.1016/S0307-4412(00)00018-2

Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., Leunissen, J.A. (2007). Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Research, 35(Web Server), W71-W74. DOI: 10.1093/nar/gkm306

World Peas

ResearchBlogging.orgYeah, I know, it is a bad bumper sticker. But how often do you actually get to use it legitimately?? Recently I came across an article that made me think back to developmental biology in grad school and the amazing work that was coming out of the giant zebrafish mutant scans.

A Mother Lode of Mutant Fish (Science 1996, may require subscription) Researchers this month are announcing the first major findings from an international project to generate thousands of mutant zebrafish with telltale embryonic defects. The faulty fish are expected to yield fundamental insights into embryogenesis, the process by which an organism’s genetic blueprint unfolds into a body that can slither, swim, or saunter.mendel_peas.jpg

Of course, this followed on the heels of the giant Drosophila screens that yielded so much information. And preceded that Nobel prize for that work

From the article: French Researchers Create Genetic Reference Collection of Pea Mutants

Senior author Abdelhafid Bendahmane, a researcher with the French National Institute for Agricultural Research’s Plant Genomics Research Unit, and his colleagues used an approach called Targeting Induced Local Lesions In Genomes, or TILLING — a targeted genetic modification based on ethane methyl sulfonate induced mutagenesis — to create a group of characterized pea mutants within one genetic background.

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