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Old 07-28-2013, 09:48 PM   #1
Fernas
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Location: Middle East

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Default Get Promoter Sequence for List of RefSeq IDs

Dear All,

I have a list of RefSeq IDs. Each ID consists of a pair of IDs (protein ID;mRNA ID) for example (NP_001135412.1; NM_001141940.1). I retrieved this list from Uniprot for different organisms (mainly mammalians).

My question is:
I want to get the promoter sequence of (+1000,-200 nt) starting at the gene start position (TSS) for each portein ID in my list. How can I do that?
Will I need to download all genomes of these organisms and get the TSS positions for all my RefSeq IDs then extract the promoters from the genomes? Any better solution?

Thanks in advance.
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Old 07-29-2013, 04:14 PM   #2
Fernas
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Default

Any answer/help guys?

I found a related thread
http://seqanswers.com/forums/showthread.php?t=10436
But, I am not sure if the methods suggested there will help because I have multiple species.

I appreciate any help that can save time in doing this task.
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