Hello Weldon, There is not a way to do this within the Genome Browser. However, you could use the stand-alone BLAT program (it is free for academic, non-profit, and personal use) to align sequence to whatever reference sequence you wish to use. See the BLAT FAQ page for more details:
http://genome.ucsc.edu/FAQ/FAQblat Also see the BLAT specification: http://genome.ucsc.edu/goldenPath/help/blatSpec.html -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/17/08 03:42, Weldon Whitener wrote: > I'm working on insertions in the human genome, and what I would like to do > is: take a bit of sequence that contains an insertion and use it as the > reference that I can then align the human reference back to. This would > show the alignment of the reference back to the insertion with the *de > novo*sequence in between. > > In essence, can I load in my own reference? > > Best > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
