Question: Finding a downstream ORF
gravatar for andrey.v.shubin
4.0 years ago by
andrey.v.shubin60 wrote:

Hi everyone,

I have a list of several hundreds of bacterial protein identifiers (e.g., WP_040242412.1), and I need to find which ORF follows downstream. Using Entrez Direct I can get genome identifiers, coordinates and strand orientation for ORFs for these proteins (e.g., WP_040242412.1: NZ_CDGZ01000012.1 109108 110151 -), but I do not know how to proceed further and inquire the databases about a downstream ORF.

All suggestions to crack this issue will be appreciated.


genome orf entrez direct • 1.1k views
ADD COMMENTlink modified 4.0 years ago by EVR570 • written 4.0 years ago by andrey.v.shubin60
gravatar for EVR
4.0 years ago by
EVR570 wrote:


I will do the following: 1. Get the entire mRNA sequence for your interested proteins which must has 5'UTR,CDS and 3'UTR. 2. Later using deep sequencing data find whether you get any coverage in 3'UTR3. 3. If you get any coverage, then extract those coverage region and validate them computationally(blast, interproanalysis, database searching, etc)

The above steps are not the gold standard but it can be a good starting point

ADD COMMENTlink written 4.0 years ago by EVR570
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