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primer3 - select primer in 3' end (Mar/25/2004 )

Hi,

Does anyone know if there is a parameter in primer3 that I can set to search only the last 750 bp of my input sequence?

Thanks in advance,

Eric

-ebensen-

Yes, you can.

There are two parameters you can use to ask primer3 to only pick primers in the last 750 bp of your sequence.

1) target region: you give for example "800,10" which means the sequence from 800-810 must be included in your PCR product.

2) Included region: you give for example "750, 500" which means the primers must be pick within 750-800 bp region.

Or you can simply paste only the last part of your sequence into the program.

Help it helps.

sage

-sage-

Thanks for the reply,

Is there a way to set the parameter in target region as ‘750 bp from the last base’, such as –750? I’m loading a file with multiple sequences – each sequence is a different length- and would rather not pull out the last 750 bp from each sequence.

Thanks again,

Eric

-ebensen-

To my knowledge, unfortunately, primer3 doesn't provide such feature. It counts position all from the begining. I understand you are doing batch processing. One thing you may want to try is to reverse complement your sequences and then specify the first 750 bp as included region.

-sage-