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Design primer from incomplete sequence...


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#1 Saiful Shakirin

Saiful Shakirin


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Posted 04 March 2013 - 12:17 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 mdfenko


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Posted 04 March 2013 - 06:46 AM

you can use a primer design tool to design a primer from the known portion of the sequence.

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#3 Trof


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Posted 04 March 2013 - 09:49 AM

Do you know what RACE and genome walking is and what is the principle behind, how to do it? You can look it up and then ask about specific details. There are surely kits for RACE, at least.

In these days, if your plant isn't especially exotic, you can help yourself by aligning the incomplete sequence you have to the know sequenc of this gene in similar plant. You may even find the sequences are very identical, design primers based on the similar plant (or several of them) and bang!.. try PCR with loose conditions to get a product for sequencing.
You can use BLAST to find these similar sequences.

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