Hi Nicolas, The multiple alignment track is built from the chain/net pairwise alignments. Pairwise alignments between assemblies that are 2X (i.e. are of lower quality) will have reciprocal-best filtering (more information in the conservation description page). These pairwise alignments are available in the Primate Chain/Net track. Syntenic filtering is done before assembling the pairwise alignments into the multiple alignment track, so the pairwise chains may still have alignments to the pseudogenes that you're looking for.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 3/9/11 5:29 PM, Nicholas Price wrote: > Hi , > > I am trying to find orthologous processed pseudogenes using the > locations of human pseudogenes and the > multiz46way-Conservation track . > > However I noticed that under the description it says. "An additional > filtering step was introduced in the generation of the > 46-way conservation track to reduce the number of paralogs and > pseudogenes" ... > I was able to find a large set of what seem to be orthologous > processed pseudogenes...at least in primates... Do you have the > alignments without the filtering step mentioned above? or the script that > produced the alignments? I was also wondering what the filtering step was?? > > > Thank you > > Nicholas > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
