OK, I don't know much things about Drosophilia but its seems that the UCSC has already computed the BLASt alignment in dm3.hgBlastTab. I've tried to link the table flyBaseGene to the human table kgXref that describes the human genes, via dm3.flyBaseGene:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D dm3
mysql> select * from
dm3.flyBaseGene as F ,
dm3.hgBlastTab as B,
hg19.knownGene as G,
hg19.kgXref as X
*************************** 1. row ***************************
description: 5'-3' exoribonuclease 2
1 row in set (0.22 sec)
I trust Compara at pretty much the highest level that I do for in silico results I haven't produced myself. Read more about how Compara gene trees are constructed here to form your own judgement: http://www.ensembl.org/info/docs/compara/homology_method.html
This is an incredible resource . How much do you trust it though? A lot of money is riding on this screen and I want to express the appropriate amount of caution to my collaborators regarding its accuracy.
This is a good approach and I've voted it up. Two issues I have with pre-calculated results are 1) When was this done and how many new genes/mRNA isoforms were not part of the comparisons? 2) What comparison parameters were used to make the assignments? Those are often not well described.