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Positive Selection on non-coding dataset (Read 785 times)
Aisha_Pisces
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Curious HyPhy user

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Positive Selection on non-coding dataset
May 17th, 2014 at 3:01pm
 
Hi,
I am interested  to detect signatures of postive selection on non-coding dataset. For that, i subjected my dataset to HyPhy 'noncodingselection.bf' using intronic sequences as neutral proxy. However, i don't seem to interpret the output.

Here is the output:

number of replicates for likelihood fitting= 10
Intron(s) used as neutral proxy with HKY85 model.
Branch specific test with foreground branch Human
NULL= Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG.
ALTERNATE= Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG. Class 3: Negative selection in BG, Positive in FG. Class 4: Neutral evolution in BG, Positive in FG.

*** Null model ***
inverse kappa: 0.00589578813346601
f0: 0.2426574443737675
f1: 0.02096646396237873
f2: 0.7363760916638536
zeta0: 0.03093970353822078
zeta1: 1

*** Alternate model ***
inverse kappa: 0.01619338026668704
f0: 0.2427677498110386
f1: 0.02096177132117792
f2: 0.7362704788677835
f3: 0.05852031028723284
zeta0: 0.0309385053561257
zeta1: 1
zeta2: 0.005907867454639304

Lk null = -9831.975230914895 Lk alt = -9831.973668884511
LRT = 0.003124060767731862
LRT p-value = 0.9554268099

Moreover, the program asked for either to apply BEB and NEB. I applied BEB and got a table as a result, having three columns named Negative, neutral and positive selection.

But i am at a loss to understand the values in those columns..

Is there any one who can simplify all this for me?? In dire need of a positive response.

Thanks!
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