Comparing two proteomes/genomes!

[pulikoti]

Hi all,

I need suggestions on how to compare two genomes, find out genes that are common between the two and those that are unique. So far i've done a pairwise alignment of each gene in genome1 with the genes in genome2 and vice versa. Kindly help. Thanks

[westerman]

I think you will need to tell us more specifically what type of help you need. Since you have the pairwise alignments of each gene in each genome then it should simple to count up the ones in 'common'. Of course 'common' is a nebulous term -- what level of homology and length do you require.

[A_Morozov]

For start, you can just call pairs of genes with alignment score above certain treshold common, and call those that don't have such pairing unique. This is grossly oversimplified approach, because unless you have some really small genomes (like viral or organellar) some genes are gonna have more than one copy. Are these the same or different or you? And what if some genes are indeed of the same function but derived from distant groups eg via HGT? And are you gonna compare anything other than gene content?
I agree with westerman - you need to tell us more about what exactly question your project must answer if you want us to give valuable advice.

[Joann]

It would be interesting to see what alternative annotations besides alignment score there might be between two evolutionarily diverse genomes that interact, say, in an ecological niche situation