Hi Jia, 1. The reciprocal best chain is made by making a chain (methods here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=primateChainNet) and then performing reciprocal best filtering. The syntenic net file was made by taking the alignment chains and netting them together (further described here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=primateChainNet). After the netting process, syntenic filtering was performed. Both the syntenic net and the reciprocal best chain could be useful to you; it depends on which method you think will be best for filtering out non-orthologous alignments.
2. You are correct, chains are sorted by score. 3. There has been substantial chromosome rearrangement even within human populations, so it is not clear if this would be a good way to filter out non-orthologous regions. While we are not funded to provide research advice, one of our developers said that it might make sense to have a cut-off for a minimum chain/net length, but that you would have to determine if it made sense to do this given your research question, and if so, what the minimum length would be. 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 6/28/11 2:52 PM, Zeng, Jia wrote: > Hi Luvina, > > Thank you for your reply and I appreciate that you guys are taking the time > to construct the file in response to my request. While waiting for the > release of the new file, I have a few additional questions: > > 1. I noticed that in the hg19 vs panTro2 directory, a syntenic net is > provided, which was obtained by using the tool called netFiilter on the > regular axtNet files and consequently is a more stringent version of the > axtNet. Could you kindly comment on the similarities and differences between > the syntenic net and rbest.chain files (other than the fact that one is a > net, the other is a chain file)? > > 2. When I carefully examined the content of the rbest.chain for hg17 vs > panTro1, I noticed that the chains are not sorted according to the chromosome > order, but it seems to me that the scores associated with the chains are > decreasing. Can you confirm this interpretation? > > 3. In the hg19 vs panTro2 syntenic net files, some entries mapped regions > from hg19's chromosome 1 to other chromosome of panTro2 (eg. chromosome 15, > or chromosome Un etc). I presume that these regions do present the best > homology but not necessarily orthology, therefore if I were to start my > orthology region search using the syntenic net, I should simply eliminate > these entries. Is this correct? > > Thank you once again. > > Best, > - Jia Zeng > > ________________________________________ > From: Luvina Guruvadoo [[email protected]] > Sent: Tuesday, June 28, 2011 12:24 PM > To: Zeng, Jia > Cc: [email protected] > Subject: Re: [Genome] Locating orthologous regions (not just genes) between > human and chimp > > Hi Jia, > > We have noted your request and will notify you once the rbest.chain file > for hg19 vs panTro3 has been released. > > Regards, > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > Zeng, Jia wrote: >> Hi, >> >> I have this question and after searching the mailing-list archive, I found a >> similar thread for which a UCSC staff member Jennifer gave a very good >> answer to: >> (https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021123.html) >> >> But my question is a bit more general than the original post so I would >> appreciate a bit more information. >> >> I need to perform a genome-wide search to locate all the orthologous regions >> (including both non-coding and coding regions) in the human genome that are >> orthologous to the chimp genome. From the original answer in the related >> post, I have an impression that to do so, the best way is to get a hold of >> the "best reciprocal alignment" between the human and chimp genome instead >> of just the single directional alignment such as the files shown in >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/axtNet/ (I kind >> of presume the single directional alignment does not necessarily imply >> orthology since some regions in the human chromosome 1 correspond to the >> chimp chromosome 15, which doesn't make sense). >> >> However I failed to locate the rbest.chain file in the newest human/chimp >> assemblies, which used to exist in earlier assembly (eg. hg17 vs panTro1). >> Could you please let me know how I can construct the best reciprocal >> alignment between human and chimp using two single directional alignments >> (human vs chimp and chimp vs human)? Can I just naively intersect the two >> single directional alignments and retain the entries that exist in both >> files? Please kindly advise. Thank you very much for your time in advance. >> >> Best, >> - Jia >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
