Distinguish between forward strand, plus strand, sense strand

Question

[tien]

Hello all,

Question 1: I'm confused about definition of types of strand and cannot find any official document about that. So I'm here to verify my understanding about them:

• Forward strand has its left-to-right respective to 5'-to-3'. And reverse strand has its left-to-right respective to 3'-to-5'
• Plus (or positive) strand is equivalent to forward strand. Minus (or negative) strand is equivalent to reverse strand
• Sense strand means it has mRNA part. Antisense strand is complementary information to sense strand which has no mRNA part. Sense strand can be on either forward (positive,plus) strand or reverse (negative, minus) strand.
• Coding strand is equiavalent to sense strand. Template strand is equivalent to antisense strand.

Question 2: Is information about reverse/forward strand in flag of SAM file equivalent to above definition of strand? Especially in result by STAR alignment.

Question 3: Does all genome database store position in term of forward strand only? For example, ensembl.

And if possible, can anyone of you share with me any official document about these things?

Thanks in advance for any help.

[tien]

I now think of definition in a different way:

Question 1:

• Forward strand and sense strand and coding strand are now the same that include mRNA part.

• Plus strand or negative strand is just a fixed reference to DNA. A mRNA can have it coding/sense/forward strand on either plus or minus strand.

Question 2: In SAM, we have flag for reverse/forward strand, we can use it to determine that if transcript and its read is on the same or different strand

Question 3: Does all genome databases store position in term of plus strand?

Answer 1

[tomas4482]

Q1 you're correct.

Q2 Flag 16 means the mate read of this read can be mapped to reference genome, which is always positive orientation. Therefore, read with flag 1 & 16 indicated the sequenced mRNA segment is on reverse strand. read with flag 1 and without 16 indicated a forward strand.

Q3 they provide both position and strandness. If you mean fasta of genome, then yes.

Check SAM document archived by samtools here: https://github.com/samtools/hts-specs

[tien]

Thanks for your comment. About question 1, do you mean my first or second thought? And about question 3, I mean the position (for example in fasta or gtf) is respective to positive strand (start is always on the left and end is always on the right). Btw, do you have any document for definition of these strands?

[tomas4482]

All answers refer to your questions in main thread, not in your comments.

Yes. position is respective to + strand.

I don't understand what you mean by definition of these strands. I think you have known what positive and negative strand mean.

[tien]

I think I know what they mean now. But I'm wondering if there exists any document that states these things officially, because I've tried but found no document.

[tomas4482]

Please read samtools and STAR documents. If you want to dig into it, you can read methodology and technical document of sequencing that you particularly interested in.

[tien]

Many thanks for your help.

Answer 2

[Buwei]

As described in GENE XIII, plus-strand and minus-strand DNA are concepts within retroviral genetics.

Retroviruses have RNA genomes, referred to as plus-strand RNA. Reverse transcriptase has the capability to generate a complementary DNA sequence known as minus-strand DNA. Besides its reverse transcription activity, reverse transcriptase can also synthesize a second DNA strand, known as the plus-strand DNA, using the minus-strand cDNA as a template.