Hello

I am a beginner in Bioinformatics and I have a problem when I read some papers.

the paper name is SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequence data and its context is related about a structural variants.

Anyway I can't figure out the meaning of strand orientation.

The word strand orientation comes from this sentence which is 

> If one of the two ends of remaining pairs has an unexpected strand orientation, the cluster is annotated as a potential inversion.

I've already know that strand orientations means just direction of DNA(5'->3' or 3'->5')

but it seems strange considering the concept of strand orientation i knew. It can't match I think..

Help the meaning of strand orientation connected with the sentence above

Thank you
You stated that "strand orientations means just direction of DNA" but that is not correct.

DNA is made of two strands (who form a double helix). They run in opposite directions. Some proteins are encoded on the positive strand, some others on the negative one.

Each nucleotide is paired to its complement on the other strand; therefore you only need to record one strand.

Check [Wikipedia][1] or some MOOC about introductory Biology.

 [1]: http://en.wikipedia.org/wiki/Dna