Hi Nicholas, I don't have any quick answers for you on how to decide whether the sequences in the multiz46way table represent truly orthologous regions in distant species. I can point you to the documentation on how the table was created, though. First look at the Conservation track description (hit "describe table schema" in the Table Browser or just follow this link: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way). The multiple alignment (multiz46way) track is created from pairwise alignments, which are displayed in the Chain and Net tracks. To see a description of those tracks, select one in the Table Browser and hit "describe table schema" or click here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=primateChainNet.
The references section in both of the track descriptions have links to several applicable papers. There's also this page on our genomewiki that has an informal discussion of chains and nets that you might find helpful: http://genomewiki.ucsc.edu/index.php/Chains_Nets To see why there are only 5 nucleotides for pteVam1 in your sample below, I recommend looking at your region in the Genome Browser and zooming out a bit. You'll see that the 5 nucleotides are actually part of a longer alignment, and that the region you are interested in mostly contains a gap. I hope this helps. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/09/11 17:03, Nicholas Price wrote: > Hi > > I am trying to identify orthologous pseudogenes using Human as the reference > genome..I am using multiz46way..Given that pseudogenes are evolving > neutrally, my question is at what evolutionary distance (0.05,0.1,0.2 > etc) can I be more sure that the sequences returned are orthologous...Have > there been any tests done?...For example given the human > pseudogene chr5:180378815-180378949 the following sequences are returned.. > The results include very distant species like the Flying fox: pteVam1. Why > is a sequence of 5 nucleotides returned? Thank you very much ...Nicholas > > >> pteVam1 > cagaa >> loxAfr3 > aatgaactattgatacacaacacggatgaatctcaaaataattattccaagtcatagaagccagaccaggaaaaaaaaaaaaaaaagaata >> otoGar1 > GAGAATATCCGGAAGATGCAGG >> choHof1 > CAGCAGCTCCGCGTGCAGGAGGCAGTGGACTCCATGGTGAAGAGTCTGGAGAGAGAGAACATCCGGAAGATGCAGG >> panTro2 > CAGCAGCTGTGGGTGCAGGAGGTGGTGGACTCCGTGGTGAAGAGTCTGGACAGAGAGAACATCCAGAAGATCCAGGTGAGCAGCCCGAGGCCCAGCCAAGGCGTGGCCAGGGTGAAAGACCAGAAAGGCGAAGGC >> macEug1 > GCTGCGGGTGCAGGAGGCGGTGAACACCATGGTGAAAGGACTGGAGCGGGAGAACATCCGCAAGATGCAGGTAGCGGC >> rheMac2 > CAGCTGTTGTGGGTGCAGGAGGTGGTGGACTCTGTGGTGAAGAGTCTGGACAGAGAGAATATCCAGAAGATCCAGGTGAGCAGCCTGAGGCCCAGCCAAGGCGTGGCCAAGGTGAAAGACCAGAAAGGCGAAGGT >> eriEur1 > CAGCAGCACCGGGTGCAGGAGGCGGTGGACACCATGATGAAGAGTCTAGAGAAGGAGAACATCCGAAAGATGCAGGTAGCCCGGCTGGGGTCGGCCAGGGCACCGCCAAGGTGAAAGCCCGGATAGGCTAATGC >> ponAbe2 > CAGCAGCTGTGGGTGCAGGAGGTGGTGGACTCCTTGGTGAAGAGTCTGGACAGAGAGAACATCCAGAAGATCCAGGTGAGCAGCCCGAGGCCCAGCCAAGGTGTGGCCAAGGTGAAAGACCAGAAAGGCAAAGCC >> papHam1 > CAGCTGTTGTGGGTGCAGGAGGTGGTGGACTCTGTGGTGAAGAGTCTGGACAGAGAATACCCAGTAGATCCAGGTGAGCAGCCCGAGAGTCAGCCAAGGCGTGGCCAAGGTGAAAGACCAGAAAGGCAAAGGC >> hg19 > CAGCAGCTGTGGGTGCAGAAGGTGGTGGATTCCATGGTGGAGAGTCTGGACAGAGAGAACATCCAGAAGATCCAGGTGAGCAGCCCGAGGCCCAGCCAAGGCGTGGCCAGGGTGAAAGACAAGAAAGGCGAAGGC >> speTri1 > CAGCAGCTCCGGGTGCAGGAGGCGGTGGACTCCATGGTGAAGAGTGTGGAGAGGGAGAACATCCGGAAAATGCAGG >> echTel1 > CAGCAGCTCCGCGTGCAGGAGGCAGTGGACTCCATGGTGAAGAGCCTGGAGAGGGAGAACATCCGGAAGATGCAGG > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
