Sequencing Tool

Shieh Lab dN/dS Tool

sequence analysis dn/ds tool

Xiaoyan Ge and Joseph Shieh

Please enter your coding sequenceInstructions


Enter number of variants
S:    N:


KEY

Number of synonymous and nonsynonymous variants (S) and (N).

Length: The length of the coding sequence.
SS: Total number of putative synonymous sites.
NSS: Total number of putative nonsynonymous sites.
dS: The number of synonymous variants/total synonymous sites (S/SS).
dN: The number of nonsynonymous variants/total nonsynonymous sites (N/NSS).
dN/dS: The ratio of S/SS and N/NSS for the given sequence.

INSTRUCTIONS

  1. This tool allows calculation of dN/dS for a DNA sequence given variant counts, and it also calculates the total number of putative synonymous and nonsynonymous sites for any sequence.
  2. Please enter coding sequence. The input sequence should be continuous DNA coding sequence, e.g. reference.
  3. Enter N and S values. For example, N and S values can be obtained by the observed synonymous and nonsynonymous variants from sequencing results of large-scale sequencing projects. For total putative sites results only, enter 0 for N and S.
  4. Submit for results.
  5. The output results are SS, NSS, dS, dN and dN/dS.

REFERENCES

Ge X, Kwok PY, Shieh JT. Prioritizing genes for X-linked diseases using population exome data. Hum Mol Genet. 2014 Sep 12. pii: ddu473. PubMed PMID: 25217573.
Nei M, Gojobori T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, et al. (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science, 337, 64-69

Last updated on 6.26.2014