Hello, The Conservation track MAF alignment can be limited by species by using the filter function and adding in the desired assembly name (one) to create a pairwise alignment. This result can be exported to Galaxy and intersected with your regions (the Table browser cannot retrieve portions of alignment block - all or none is the result if an overlap or region query is made).
The chain or net track can be used, but used alone, they do not represent the same type of data result. For a chain or net track, the comparison is from species A->B ordered alignments. In the conservation track, the data is filtered for A<->B synteny. If you use just chains or nets, you will likely need to use the data as an input to your own processing, not as a final result. See the phyloP subtrack information concerning scores generated by PHAST. You should be able to create scores for any subset of the data that is already aligned. Be sure to note that the new 46-way is available in the updated Human GRCh37 (hg19) assembly. The Conservation MAF or PhyloP data can also just be downloaded: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/ Some prior mailing list questions that provide related information: https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019178.html https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019526.html https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019616.html We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Maxim" <[email protected]> wrote: > From: "Maxim" <[email protected]> > To: [email protected] > Sent: Sunday, December 13, 2009 3:22:47 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] extraction of conservation scores for specific genomes > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
