2. The following is a small portion of a coding gene in two species codon# 1 2 3

Question

2. The following is a small portion of a coding gene in two species

codon#

   1 2   3    4   5    6   7   8 9   10 11 12   13 14 15   16 17 18   19 20

1 GAA ACC AAA TTC GCC GCT GTA GCA GAA GAA CGT GAA CAA TGC GAT ACC TAT ATA GTT AGC

2 GAA AAG AAG TTC GCG GCG GTT GCA GGA GAA CGT GGG CAG TGT GAG ACT TAT GCG GTT AGC

using the above translation reading frame of the sequences to calculate:

c)The rate of nonsynonymous substitution (Ka). (using counting method with unweighted approach and JC model).

d)The rate of synonymous substitutions (Ks). (using counting method with unweighted approach and JC model).

e)The ratio of Ka and Ks (Ka/Ks= )

f)Recalculate “c” to “e” if (1) 2nd codon is weighted as 80% for pathway with synonymous substitution and 20% for pathway without synonymous substitutions; and (2) 18th codon is weighted as 10% for pathways without synonymous substitution and 20% for pathways with synonymous substitutions

Explanation / Answer

[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2)

[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2, ...'GeneticCode', GeneticCodeValue, ...)
[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2, ...'Method', MethodValue, ...)
[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2, ...'Window', WindowValue, ...)
[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2, ...'AdjustStops', AdjustStopsValue, ...)
[Dn, Ds, Vardn, Vards] = dnds(SeqNT1, SeqNT2, ...'Verbose', VerboseValue, ...)

Variance for the synonymous substitutions rate(s).

Here non synonymous =5 synonymous

Synonymous=15

the rates are calculated by software generated programs

Dn Nonsynonymous substitution rate(s). Ds Synonymous substitution rate(s). Vardn Variance for the nonsynonymous substitution rate(s). Vards

Variance for the synonymous substitutions rate(s).

Related Questions

Navigate

• Browse (All)
• Browse 2
• Subjects

---

---

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.