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. Thanks -Ed _______________________________________________ Methods mailing list [email protected] http://www.bio.net/biomail/listinfo/methods
