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
