Do I need to search for the complementary sequence when using regex?

Question

[jamie.pike]

Ok, prepare yourselves, this might be a very stupid question... If I am searching using a regex in an assembled genome, e.g. "ATCG", do I also need to search for the complementary sequence "CGAT" or will the assembly read 5′→3′?

[Joseph Hughes]

If you mean you are searching in fast sequence of a contig or a consensus sequence, then yes you will need to search for both. Generally if producing an assembly using denovo tools, the program will not know what is the correct 5' to 3' etc... If you are searching in a SAM/BAm of aligned reads against a consensus or reference, then generally you will have reads mapping in both directions.

Answer 1

[JC]

short answer: Yes

long answer: DNA encodes information in both chains, also you assembly is most likely not oriented as de-novo assemblers just assemble without specific direction