Dear List, I would like to create my own multiple alignment file for hg18, mm9, rn4 and canFam2 from UCSC pairwise alignments by using Multiz/TBA aligner. I got following several questions which I am not sure yet after a broad reading. It would be very appreciated if you could shed some lights on them:
- Which aligner, Multiz or TBA, would be better if my purpose is to study the motif conservation on the final MAF. - Multiz/TBA takes pairwise alignment in .maf format. While from UCSC I can only find pairwise alignment in .chain, .net or axtNet format. I found there are programs available in Kent source to do the format convert: chainToAxt, netToAxt or axtToMaf. My question is which pairwise format should I download to create multiple alignment? - Is there anything else I missed here during this process? Thank you very much in advance! Kind regards, Yuan _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
