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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ppppppxxxxxxxxxxxxxxxxxxxxxxppppppppp
3 answers
Update: here is an example with XSLT+UCSC-Das-Server+awk generating a custom BED file for the UCSC:
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written
by
Pierre Lindenbaum
Use Geneious. It uses primer3 for primer design, nicely visualizes everything and trial version can be downloaded for free.
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written
by
Biomonika (Noolean)
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.
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yes, but I prefere a Graphics user interface .
And I m not sure that primer3 generate multiple primer.
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"
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