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Old 04-15-2017, 01:06 PM   #1
cktheory
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Location: Pennsylvania

Join Date: Jan 2015
Posts: 3
Default Motif search upstream of ORFs

Hi All,

I am having some issues filtering out results from motif searches that I've done and I am wondering if anyone can suggest a better tool.

I need to find a specific motif sequence but limit my search to intergenic regions right before an ORF. The target sequence should be a ribosome binding site of an mRNA. It would be great if the output of this search listed the motif sequence and the name/identifier of the gene it was directly upstream from.

It is for a Pseudomonas genome and at this point the best I can think of is to identify the intergenic motifs, map them to an annotation file, and then manually record the adjacent gene but there has to be a better way. Any suggestions would be greatly appreciated.

Thank you!!
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intergenic motif, motif finding, orf finder, ribosome binding site

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