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Design primer from incomplete sequence...

Started by Saiful Shakirin, Mar 04 2013 12:09 AM
Primer

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#1 Saiful Shakirin

Saiful Shakirin

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Posted 04 March 2013 - 12:09 AM

Hi guys....Posted Image

Im new here and i really really really need your help... My research is about to complete the incomplete sequence of phenylalanine ammonia lyase gene from a plant.....i already have the incomplete sequence of the gene..my supervisor asked me to design primer from the sequence..my project involve RACE, RTPCR and genome walking...I really dont know how to design primer from incomplete sequence of gene...i hope you guys can help me... Posted Image

#2 bob1

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Posted 04 March 2013 - 12:14 AM

If you have sequences for this gene in other species you can align them all and take the "consensus" sequence and use that for designing  primers.

#3 Saiful Shakirin

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Posted 04 March 2013 - 12:22 AM

Align with other sequnces by using blastn from NCBI is it? how to know which part of sequence i need to choose to design primers?
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