Hi, How to design primer sequences from LINE1 retrotransposons?

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Paul Rutland

the settings in blast may exclude known repeat sequences for primer design as these will amplify thousands of similar amplimers so check the default settings

Frederic Lepretre

I agree with Paul, and since LINE1 is not a gene but some repeated sequences along the genome, you won't success in processing blast.

Real Sumayya Abdul Sattar

So how do we blast the LINE1 sequence then? How do we design pimers?

whether LINE1 is repeated along the genome does not mean that the sequence of each one is perfectly conserved. and THAT is an issue for you. you'll need to proceed with a consensus sequence:

https://www.biorxiv.org/content/10.1101/594200v1.full.pdf

all the best

frred