What Are The Main Uses Of A Consensus Sequence?

Question

[Sheila]

Forgive me for this question, but could anyone explain to me what are the main uses for a consensus sequence? In other words, what kind of research requires the use of consensus sequences?

If you have VCF files do you need the consensus sequence?

Answer 1

[lh3]

In the context of NGS analysis, consensus sequences provide regions where we can make confident calls, which is missing from variant-only VCFs. They are mostly useful for popgen. For example, you can compute heterozygosity from a consensus sequence, but you cannot do the same with a variant-only VCF.

Answer 2

[Jordan]

I think consensus sequence represents which amino acid or nucleotide appears the most frequent in a position. I have seen it used most during estimating motifs and also after multiple alignment. And most of the splice sites are represented by consensus sequences too.

A typical consensus sequence looks like this:

AG[TC]T[CG]NSA

And I'm not sure about the vcf files question. It depends on the kind of analysis you are doing and why you need it I guess.

[Sheila]

So if you have the bam (assembly) files, do you need (or want) the consensus sequence files?

[Jordan]

I never needed the consensus files. Which analysis are you working on? Why do you think you need consensus files?

Answer 3

[Alex Reynolds]

A motif usually has a consensus sequence with high information content at most bases. One could use a consensus sequence to demonstrate that a set of genomic regions (obtained via lab or computational methods) constitutes a particular motif.