I there to all.
I'm doing some personal research about some genomic sequence. I have like 600 orthologues sequence, taken via pycogent from a genomic alignment between human and six other primates.
I was asking my self which is the best approach to get the conservazion scores for that regions, in base by base way. I was thinking about aligning them with clustalw, and then calcolate the conservation score via phastCons.
A quik look at the phastCons guide says that its a good idea let phastCons estimate the free parameters in case the sequence are small and with less than 12 organism. (That this is my case)
The question is, it is that a good approach? Or it is better to get the conservation scores directly from the popular UCSC tracks, istead of calculating them by myself?
And if this is the best approach, there is some way to programmatically get the scores via script? Es via Python?
The lenght of each sequence i have is not so much around 1kb. Bad idea go for a calculating approach?
Better use phastCons or get data from UCSC? (If this is the case how to data mine them via Python using genomic coords?)
Thanks in advice
