what is the dn/ds course hero

What does it mean when dn/ds =1?

What is the ratio of dn/ds?

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Evolutionary Biology: What is the dN/dS ratio? - Quora

Answer (1 of 2): Evolution is well-known to be driven by natural selection. Organisms with changes in their genetic code that result in a better phenotype will have more offspring and thus propagate these beneficial changes through their population. Whether a phenotype (and thus the underlying ge...

How to calculate dN, dS and dN/dS value by MEGA program? - ResearchGate

I have performed a codon based-Z test (MEGA) on a protein coding gene alignment from 30 species to compare the dN-dS values used as a measure of selective pressure indicating neutral mutation ...

A beginners guide to estimating the non-synonymous to ... - PubMed

The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale-from the small genomes of viruses, bacteria, and para …

How can I calculate dN/dS within and between species?

- For within-species, there is just not enough information to reliably estimate dN/dS. Usually, population-level work applies nonsynonymous and synonymous nucleotide polymorphism, which is just ...

The relationship between dN/dS and scaled selection coefficients

Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct methods relate to one another remains largely unknown. Here, we elucidate the relationship between two widely used phylogenetic modeling frameworks: dN/dS models an …

What does it mean when dn/ds =1?

If dn/Ds =1, it could be that the sequence is evolving neutrally.

What is the ratio of dn/ds?

However in real data, you will never see this ratio going close to 1, because most amino acid positions on the sequence are functionally constraint. In other words, almost all coding sequences on average should have 0 < dN/dS < 1. This ratio is usually between 0.2 to 0.3 on average for typical proteins. Nevertheless, there could be sites under positive selection, whose signal may be "masked" by averaging across the whole sequence. This is why people developed "site-models" to allow for rate heterogeneity of dN/dS across different amino acid positions (see CodeML).

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uses Pal2Nal briefy, say you have a fasta file with 10 aa sequences and corresponding nucleotide sequences, yoiu can align the aa sequences and get an output in fasta format. the aligned aa sequences can be used to get a codon-aligned nucleotide sequences in fasta format.

Popular Answers (1)

While Nei-Gojobori and other "counting" methods (all of those you name) made a major contribution to in field of computational molecular evolution, much better alternatives now exist. Do you only have pairs of sequences? If so then use maximum likelihood to compute dN and dS.

All Answers (15)

I used the single likelihood ancestor counting (SLAC), the fixed effects likelihood (FEL), and the random effect likelihood (REL) methods implemented in the HyPhy package See the webpage: http://www.datamonkey.org for details. As an input you use ClustalW alignments of nucleotide sequences.

What does it mean when dn/ds =1?

If dn/Ds =1, it could be that the sequence is evolving neutrally.

What is the ratio of dn/ds?

However in real data, you will never see this ratio going close to 1, because most amino acid positions on the sequence are functionally constraint. In other words, almost all coding sequences on average should have 0 < dN/dS < 1. This ratio is usually between 0.2 to 0.3 on average for typical proteins. Nevertheless, there could be sites under positive selection, whose signal may be "masked" by averaging across the whole sequence. This is why people developed "site-models" to allow for rate heterogeneity of dN/dS across different amino acid positions (see CodeML).