<p>When we sequence genomes, the individual reads come from both strands, and that also applies for assembled sequences* (contigs / scaffolds). Therefore for most of the genome assemblies out there, strandeness of individual scaffolds is actually an arbitrary property, and reverse complementing any sequence will generate an equally valid representation (with reverted coordinates).</p>
<p>The coordinates of the reverse complementary k-mer matches depend on the notation. Usually, the notations are still in the coordinates of the reference, for example, blast gives for reverse complimentary strand matches the <code>from</code> subject coordinate greater than the <code>to</code> coordinate. Some others are denoting &quot;the leftmost&quot; position and strand encoded in a different column (e.g. <a href="https://samtools.github.io/hts-specs/SAMv1.pdf" rel="nofollow noreferrer">sam</a>).</p>
<p>*perhaps with the exception of chromosomal level assemblies</p>

CC BY-SA 4.0
2021-09-26T21:58:24.343Z
Do you have any suggested reading for insight on composing a single sequence from both strands? I feel like that's a big mental roadblock for me.
Moo
CC BY-SA 4.0
2021-09-27T09:50:51.487Z
To be completely honest, I don't! I would be looking out for assembly literature (especially of short reads). I will also try to keep my eyes open and let you know if I run into something.
Kamil S Jaron
CC BY-SA 4.0
2021-09-26T17:43:00.057Z
2021-09-26T17:43:00.057Z
Kamil S Jaron
<p>When looking for repeat patterns in a DNA sequence, we can look for the pattern and its reverse compliment with up to <code>d</code> mismatches. However, why do we look for reverse compliments if we're analyzing a single DNA strand?</p>
<p>I thought about it and my guess is that this lets us analyze both strands of DNA. For example, if we find the reverse compliment at position <code>x</code>, that means that the other strand of DNA has the pattern at position <code>x - pattern.length</code>.</p>
<p>Is that correct?</p>

<k-mer>
Why do we count reverse compliments when counting kmers in a single DNA strand?
# Why do we count reverse compliments when counting kmers in a single DNA strand?

(Asked by: username_0 on 2021-09-26)

When looking for repeat patterns in a DNA sequence, we can look for the pattern and its reverse compliment with up to `d` mismatches. However, why do we look for reverse compliments if we're analyzing a single DNA strand?

I thought about it and my guess is that this lets us analyze both strands of DNA. For example, if we find the reverse compliment at position `x`, that means that the other strand of DNA has the pattern at position `x - pattern.length`.

Is that correct?

**Tags:** k-mer

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## 1 answers

### Answer by username_1 on 2021-09-26. Score: 3 | Accepted answer

When we sequence genomes, the individual reads come from both strands, and that also applies for assembled sequences\* (contigs / scaffolds). Therefore for most of the genome assemblies out there, strandeness of individual scaffolds is actually an arbitrary property, and reverse complementing any sequence will generate an equally valid representation (with reverted coordinates).

The coordinates of the reverse complementary k-mer matches depend on the notation. Usually, the notations are still in the coordinates of the reference, for example, blast gives for reverse complimentary strand matches the `from` subject coordinate greater than the `to` coordinate. Some others are denoting "the leftmost" position and strand encoded in a different column (e.g. [sam](https://samtools.github.io/hts-specs/SAMv1.pdf)).

\*perhaps with the exception of chromosomal level assemblies

> **Comments:**
> **username_0**: Do you have any suggested reading for insight on composing a single sequence from both strands? I feel like that's a big mental roadblock for me.  
> **username_1**: To be completely honest, I don't! I would be looking out for assembly literature (especially of short reads). I will also try to keep my eyes open and let you know if I run into something.  

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