Hi Jia, The rbest.chain file for hg19 vs panTro3 is now available here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/reciprocalBest/
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/28/2011 10:24 AM, Luvina Guruvadoo wrote: > 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
