Primers design without annotation.

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JackBean
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Post by JackBean » Sat Aug 21, 2010 8:04 am

what about BLAST with the sequence you found? The other homologues might be annotated as hypothetical or something else...
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

bleunven
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Re: Primers design without annotation.

Post by bleunven » Wed Aug 25, 2010 8:20 am

Hi magicsiew,
In addition to a BLAST, may be you can try a tblastn, using the Arabidopsis, rice or tobacco protein sequence as Query. Restrict your search to EST (in DATABASE) and to your plant of interest (in ORGANISM).
Like this you can pick mRNA sequences and so use them to design specific primers.
Regards,
Christophe

magicsiew
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Post by magicsiew » Thu Aug 26, 2010 12:46 pm

Hi Bluenven,thanks for the suggestion. ^^

kimsmarkin
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Re: Primers design without annotation.

Post by kimsmarkin » Wed Sep 22, 2010 7:07 am

I am designing a primer targeting a gene that is without annotation in GenBank. What methods should I go through the related model plant as a reference? Incidentally, the gene is one of my goals from a plant.
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magicsiew
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Post by magicsiew » Wed Sep 22, 2010 10:04 am

Kimsmarkin.

Find the gene that u are targeting of related plant that are available from GenBank. Find as much as u can and locate the conserved region, use the conserve reason to design ur primers.

Go through the method to design Degenerate Primers from the web for more detail.

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