Nice way to view primers amplicon on hg19

Question

[sacha]

Hello,

I need to design primers for a large region of DNA, like 5000 bases. Then I have to create many primers with overlap! I can do it with primer3.

But now, I want a nice way to see all my amplicon aligned on my Sequence target.

Something like :

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[sacha]

yes, but I prefere a Graphics user interface .

And I m not sure that primer3 generate multiple primer.

[Pierre Lindenbaum]

well it would be easy to transform the primer3 output to a BED file using awk. Can you please provide a output, and name your input sequence using something like "SEQUENCE_ID=chr17:10100-10653"

[sacha]

It looks great. But What do you use to render BED file?

My sequence is the Intro of GJB2 of human in hg19 : 13:20763739-20766928

Answer 1

[Pierre Lindenbaum]

Update: here is an example with XSLT+UCSC-Das-Server+awk generating a custom BED file for the UCSC:

Answer 2

[Biomonika (Noolean)]

Use Geneious. It uses primer3 for primer design, nicely visualizes everything and trial version can be downloaded for free.

Answer 3

[seidel]

You could easily view this information using either the UCSC genome browser or IGV from Broad. At UCSC you can select the human genome and upload a BED file (or various other formats, there are some nice renderings allowing you to draw a thin line connecting the primers, color them, etc.) to view the results as a track. If you want to share the results with others, there's a way to do that as well. With IGV you can simply drop your BED file onto the IGV window and see it as a track.