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
