Comparison of gene structure - (Dec/20/2011 )

Hello everyone,

I have two genomic sequences, and I would like to know if there is any relationship between them regarding the protein coding genes (same proteins?, same order?). They definitely contain mutations on the nucleotide level, so a simple nucleotide BLAST with two sequences as queries is a bit pointless. They are already annotated, so I could theoretically check the corresponding Genbank-Files and look up each and every entry there and do protein BLASTs with the sequences, but that would "a bit" tedious. Moreover, I don't trust automated annotations. My question therefore is: does anybody know a good program that translates two sequences in all reading frames and compares the results?

Thanks for suggestions in advance!

Greetings
Freemason

Have a look at the UCSC BLAT site, they do alignment of genomic fragments.