Positive Negative Strand

Question

[freenaiss]

hello, according to wiki answers this is the definition of + /- strand :

The positive strand of DNA is the one whose sequence contains the instructions for building a protein. The negative strand merely contains the complementary sequence, according to the base-pairing rules (A pairs with T, C pairs with G); the negative strand is not normally transcribed into RNA nor translated into protein.

I've got a .bed file that contains the following information:

           **start  end     gene          strand**
NC_011191    3829    3899    trnI(gat)        +
NC_011191    3898    3969    trnQ(ttg)        -

for the first line there is a + beneath strand column, and the second line has - . I want to extract the genes' sequence from the fasta file for nc_011191. according to the above definition i got confused : shall I for the second gene (-) take the complementary of the sequence in fasta file ? or something else ? thank you in advance

Answer 1

[Heikki]

That wiki answer might be right if you are thinking of the DNA coding sequence of a gene, only.

When you have a chromosomal DNA reference sequence, all the numerous sequence features like genes can be on both strand. The reference orientation is entirely arbitrary.

When the strand is indicated as minus, you extract the sequence between the start and end locations and take reverse complement of that to get the correct feature sequence.

[chaudharyc61]

Hey I have a question, so if i want to do a motif analysis of a set of gene ids i should consider the positive and negative strand orientation too, for negative strand i should take end+500 positions and fro positive strand start+500 position, right?