6827eaab28004c74be351b4bcb4316264dc42b89 galt Wed Jun 12 01:41:12 2019 -0700 Small html errors found by htmlCheck diff --git src/hg/makeDb/trackDb/hiv/vax003PosSel.html src/hg/makeDb/trackDb/hiv/vax003PosSel.html index c3a401f..182235d 100644 --- src/hg/makeDb/trackDb/hiv/vax003PosSel.html +++ src/hg/makeDb/trackDb/hiv/vax003PosSel.html @@ -44,34 +44,36 @@ test implemented in PAML in the presence of recombination. General conclusions from these analyses indicate that excessive recombination (ρ = 0.01), like usually observed in HIV sequences, can cause false positives in the Bayes test and makes the LRT unrealistic as it often mistakes recombination as evidence for positive selection. The LRT test that compares models M7 and M8 seems to be more robust to recombination and the detection of sites under positive selection seems to be less affected by recombination. Nevertheless, a new coalescent model has been recently described that estimates the <i>d</i><sub>N</sub>/<i>d</i><sub>S</sub> ratio in the presence of recombination and hence generates simultaneous estimates of ω and ρ using Bayesian inference (Wilson <em>et al</em>. 2006). Such a model is implemented in omegaMap and has been applied to our subtype and vaccine and placebo samples. We ran omegaMap under a constant model for variation (i.e., all sites are assumed to share common ω and ρ) and the following parameter settings: +<UL> <LI>N° orders = 10</LI> <LI>N° iterations = 10<super>6</super></LI> <LI>thinning = 100</LI> <LI>priors = improper inverse</LI> +</UL> </P> <H3>Results</H3> <P> Selection pressure, as indicated by the <i>d</i><sub>N</sub>/<i>d</i> <sub>S</sub> ratio per gene and per site, and the proportion of sites under selection (p) was high for both subtypes, although subtype B showed higher values than subtype AE for both parameters. The Bayesian approach detected numerous sites under selection (n) in both datasets, although up two times more positively selected sites were observed in subtype AE than in subtype B. These differences are probably a consequence of the uneven sample sizes of these two datasets (181 and 29 sequences, respectively). Simultaneous estimates of selection and recombination also showed higher <i>d</i><sub>N</sub>/<i>d</i><sub>S</sub> estimates for subtype B than for subtype AE; the recombination rate (ρ),