Primer design if sequence is unknown for organism
Posted 26 October 2009 - 02:53 AM
I'm very new to the primer design story and for my first experiment I already got a difficult one to crack, hopefully someone can help.
I'm designing primers for a RT-PCR to measure mRNA levels of a number of genes in Sheep ( Ovis) lung tissue.
The problem is that the sequences are not yet known in sheep. I based my primer design on Cow (Bos) but again there are only 'predictions' of the sequences.
I don't know how valid these are and if I should design my primers based on these sequences??
I can also use Mouse sequences ( are known) but if I blast my primers then should a good primer also have similarity with the prediction of the Cow sequence??
Can anyone help me?
Posted 26 October 2009 - 03:45 AM
according to this, both the aniomals have more than 90% maps similar so best luk and acc to me you can go ahead using bovine as your reference and tryin it out for sheep!!!
Posted 26 October 2009 - 04:39 AM
Posted 26 October 2009 - 04:50 AM
Posted 26 October 2009 - 12:02 PM
I'm now using PerlPrimer. That program does not have an option to select where you want your primer designed.
Posted 28 October 2009 - 07:03 AM
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