Dear UCSC,
In addition to the reply from previous post.
################
Hello again, Wen,
We just display the data and allow you to draw your own conclusions
about
significance. That said, the MAF scores are not a good measure of
conservation
-- you might consider looking instead at additional analysis methods to
determine this.
For example, you could view the "Most Conserved" track in the genome
browser.
This track shows predictions of conserved elements produced by the phastCons
program based on a whole-genome alignment of vertebrates, and for the
placental
mammal subset of species in the alignment. They are based on a phylogenetic
hidden Markov model (phylo-HMM), a type of probabilistic model that describes
both the process of DNA substitution at each site in a genome and the way this
process changes from one site to the next.
I hope this information is helpful to you. Please don't hesitate to
contact
the mail list again if you require further assistance.
###################
I would like to know if there is any measure ot threshold score, which
can give us a rough idea about how well the sequence is conserved.
When we look at the score, some have -ve value, while some have +ve
and 0 value.
Does all -ve score means they r not very conserved (by eye it looks
like they r not conserved).
BUt for +ve score, is there any sort of threshold which determines
whether the sequence in the alignmnet is highly conserved or not.
regards
Chirag
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