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
