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 -- The oppressed become the oppressors Paulo Freire (1921-1997) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
