Dear UCSC genome user, I want to get multiple alignment for human, mouse, rat, cow and chicken. I found there is a multiple alignments of 16 vertebrate genomes with Human on UCSC. Because there are more genomes than I want, so I try to use the "maf_order" program from Miller's lab to exclude genomes I don't want, but after reading all the documents and codes, it looks like maf_order just deleted unwanted genomes without re-doing the multiple alignment. Could someone help me to clarify that whether it is still a real alignment after maf_order?
Another question is I downloaded upstream5000.fa from UCSC for all above 5 species. I would like to do multiple alignments of these upstream sequences. Apart from all-to-all alignment, is there other way I could do the multiple alignment? I found upstream5000.fa uses Refseq id (NM_XXXXX), which is different across species. How could I extract upstream sequences from different species corresponding to the same gene so that I only need to align 5 upstream sequences each time? I appreciate very much for your reply! Thank you very much in advance! Yuan ------------------------------------------- Yuan Hao PhD student Conway Institute University College Dublin Belfield, Dublin 4, Ireland E-mail: [email protected] ------------------------------------------- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
