Hi, I wonder whether there is a chance to extract conservation scores via UCSC, especially conservation between distinct genomes. In my case I have a lot of transcription factor binding sites (in GALAXY and as custom tracks in UCSC browser). I know how to use the table browser to extract for example PhastCons scores. But this seems to be limited to 7 or 8 tables encompassing 12-44 different genomes. Does this mean I have to produce my own conservation scores in case I'm just interested into the 3 genomes of human, rat and mouse?
The other option would be to extract pairwise sequence alignments. Is this possible with UCSC, let's say starting with .bed files with 5000 20bp intervals, to extract the pairwise alignments of those human regions with mouse and/or rat genomes? I'd be glad in case someone could point me at the right direction. Maxim _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
