Hey Nicholas, This would depend on when the pseudogene was inserted/duplicated. Our filtering is designed to remove alignments to DNA inserted after the common ancestor of the two species being compared. If a retrogene was inserted before the common ancestor, then it should appear in our alignments, just as a segmental duplication before the ancestor would.
Of course we don't actually know what DNA has been inserted, so our filters use the heuristics previously mentioned. We think the syntenic filtering using the net to measure overall synteny is a pretty good filter. The reciprocal best filter is much weaker because the scaffolds don't contain as much information about order and orientation of the DNA, so we end up removing a lot of alignments between DNA that probably was duplicated in the common ancestor. I hope this answers your question. If not, please respond to this list. Brian On Sat, Mar 12, 2011 at 6:13 AM, Nicholas Price <[email protected]> wrote: > So, > > In other words the processed pseuodgenes that are more likely to be > filtered out are the paralogous ones. > > Nicholas > > On 11 March 2011 19:23, Mary Goldman <[email protected]> wrote: >> 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 >>> >>> >>> >>> >>> >> > > > > -- > The oppressed become the oppressors Paulo Freire (1921-1997) > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
