Using the in-Silico PCR (isPCR) tool in the UCSC Genome Browser

This tutorial describes the isPCR tool and demonstrates how to use it for predicting the size and location of PCR products and visualizing the genomic location on the genome. The tool operates on DNA templates for all organisms and DNA or RNA on human and mouse. It also demonstrates how to use the Browser to obtain DNA sequences from the genome.
0:40 Set the Genome Browser to hg19 defaults
1:08 Navigate to a gene (CYP2D6) to obtain DNA for primers
1:46 Get DNA with exons annotated
2:40 Obtain primers for PCR from exons
3:25 Use primers to predict amplicon size from genome assembly
4:12 Observe amplified DNA in Genome Browser
5:32 Use primers to predict amplicon size from RNA template
6:36 Observe RNA results in Genome Browser
transcript: genome.ucsc.edu...

[@aaronmay-zhang3555]

Thanks for the vid- answered my question as to what the "UCSC Genes" function means, which I wasn't able to find anywhere else on the internet!

[@arresteddevelopment2158]

I need to learn how to do this pronto! Very important Bioinformatics tool!

[@mariajosesantiago8839]

Excellent demo!!! I have a question. What are the criteria that you use to select 3rd exon? I want to do the in silico PCR, but by gene of interest has 5 exons and I am not sure which one to pick.

[@lhlv3512]

very good

[@robertkuhn6811]

> Only human genome is amplified via ucsc insilico pcr,. How we amplify bacterial genome or others
any animal ucsc hosts can be template for isPCR. see screen at 3:30 in the vid. ucsc does not host bacteria, so that part of your comment is correct. for now. this may become possible in the next year. watch genome-announce mailing list for info: groups.google.com/a/soe.ucsc.edu/g/genome-announce .

[@Thunder-ut5jr]

how to log in to the text file?

[@BR-hi6yt]

Easy