Question: What is the meaning of alignment strand plus/minus in blastn?
gravatar for saadleeshehreen
21 months ago by
saadleeshehreen70 wrote:


I am intended to analyze the promoter sequence of my gene of interest (GOI). I extracted the promoter sequence (200 bp) by using a in-house tool. Some portion of the promoter (90 bp) came from upstream gene( it could be putative as no known annotation for the protein).The artemis view of .gbk file show the upstream gene of GOI is opposite direction, that's mean it is from different operon. As, I can't verify whether the promoter sequence is correct or not, I blasted the sequences with the genome. The alignment strand was plus/minus.The result is also same with GOI. But with that upstream gene the alignment strand was plus/plus. What does it mean? Is the promoter sequence correct? or I need to do complement of it?

blastn • 1.7k views
ADD COMMENTlink written 21 months ago by saadleeshehreen70

plus/minus, normally means that it is the reverse strand that is matching.

What are the orientations of the genes you're looking at?

ADD REPLYlink written 21 months ago by lieven.sterck7.9k

Thanks. My GOI is in the integrated phage/plasmid ( not sure!), so in some genomes they are same orientation of upstream genes ( in those cases, the strands were plus/plus for both of the promoter and GOI). But whenever the upstream genes are in opposite orientation, the strands were plus/minus for both of the promoter and GOI, but plus/plus for upstream genes.

ADD REPLYlink written 21 months ago by saadleeshehreen70
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