Tutorial:Video: Alternative Splicing and Primer Design

Question

[Nowlan Freese]

"Focus on a Feature: Alternative Splicing and Primer Design"

This Focus on a Feature has finished. You can find the recording here:

https://www.youtube.com/watch?v=1LUszUX2wuA

Program:

1. Introduction to IGB
2. Loading data sets
3. Navigating through a genome
4. Viewing alternative splicing
5. Designing and visualizing primers

Integrated Genome Browser (IGB)

IGB is a highly interactive, fast, and easy to use desktop genome browser, which is used to view and interact with sequence data from reference genomes, gene models, and alignments. Common data sets include RNA-Seq, ChIP-Seq, and other genome-scale projects. IGB can be used to produce publication quality images from genome scale data sets, and is provided FREE. IGB has a dedicated support staff and is continuously updated with new functionality.

If you have questions or need assistance, contact us at:

Nowlan Freese [e-mail]

Ann Loraine [e-mail]

*Please test-run IGB before the tutorial. To download and start IGB, go to bioviz.org and select the "Download Now" link. Once IGB starts, choose Help / Tutorials for a quick introduction to IGB.

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Answer 1

[pengchy]

Hi Nowlan Freese,

Is it possible to use IGB to design primers for alternative splicing events? The following page is empty: https://wiki.transvar.org/display/igbman/Primer+Design

Best,
Pengcheng Yang

[Nowlan Freese]

Hi Pengcheng Yang,

There is currently no way to design primers from within IGB. My advice would be to use IGB to identify regions of alternative splicing, and then use primer 3 to pick primers.

1) Identify alternative splicing event of interest in IGB.

2) Copy the DNA sequence directly from IGB and paste it in primer 3 (http://biotools.umassmed.edu/bioapps/primer3_www.cgi).

3) Use primer 3 to pick primers.

4) Visualize the primers in IGB using the Advanced Search tab to verify that they capture the alternative splicing event.

We're in the process of greatly expanding support for user developed plug-ins in IGB. The page on primer design in the IGB user's guide is a placeholder at the moment, but is a feature we would like to add in the future.

Nowlan

[pengchy]

Hi Nowla,

Thanks for your reply. It will be useful to visualize the primers on alternative splicing exons using IGB.

Pengcheng