comparative genomics

Ed Siefker via (by ebs15242 from
Fri Dec 13 16:49:05 EST 2013

I am looking for a comparative genomics tool that will take an input sequence
search for homologous sequences across a (large) number of genomes,
report a total homology score, and flag significantly conserved regions.
Where's a good place to get started?

I tried a few tools already without much luck.  mVista complains about my
query being too large when I submit just one chromosome.  CoGe BLAST
reports small HSPs instead of the full length alignments I'm looking for.  The
SLAM web server seems to be gone entirely.

Are there any existing tools that do what I want here?  Should I start working
on coding something up with PERL and Ensembl Compara?  If I use PERL,
I'm guessing I'd want to:

locate my sequence in the human genome
use the blastz-net alignments to find the same coordinates in other species
download the corresponding sequences
align with Clustal.

Does that make sense?   Any nudges in the right direction would be appreciated.

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