Hello Zhenguo,
Thank you for using the UCSC Genome Browser and for submitting your question regarding a genome alignment among D. simulans (Dsim_r2.01) and D. melanogaster (dm3).
Since D. simulans (Dsim_r2.01) does not yet exist as a genome assembly in our browser, we do not have alignments to D. melanogaster (dm3). It is likely that we will have these data in the future - though completion time for the updated D. simulans assembly is currently unknown.
Until then, you can follow
this "Whole Genome Alignment" wiki page and create your own liftOver files to convert annotations.
You can also
search "Whole_genome_alignment_howto" in our Genome Browser forum archive for related information.
As you may already know, we do have alignments among droSim1 (D. simulans, Apr. 2005) and dm3 (D. melanogaster, BDGP Release 5, April 2006):
there are links to the following 2 locations where you can find alignment files:
We have a work in progress - an automated
Invertebrates Assembly Hub. This hub pulls data from Genbank genome assemblies. If you search the
Invertebrates Assembly Hub for accession "
GCA_000754195.2" (19 Sep 2014, Dsim R2.01, Drosophila simulans) you will find a link in the 3rd column, "common name" which will load this prototype hub:
Thank you again for your inquiry and for using the UCSC Genome Browser. Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below: