Good Afternoon Eric: You can read the description of the methods used to generate these alignments in the description page for this track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm3&g=multiz15way Pair-wise alignments of each insect to D. melanogaster were performed with the blastz aligner: (now replaced by lastz) http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html Those pair-wise aligments were put together in the multiple alignment with multiz: http://bio.cse.psu.edu/dist/tba.pdf UCSC generated this multiple alignment. --Hiram earleyej wrote: > Hello, > I am working with your 14 insect CDS alignment using D. melanogaster as > the reference. The files I'm talking about are here: > http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/alignments/ > > How were these file generated explicitly? I assume that some nested BLAT > routine was used. How were the alignments then cleaned? Who actually > created these files? > > Thank you very much! _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
