Protein Sequence Homology Score, Align Or Blast

Question

[ewre]

Hi,

I want to get homology scores for every pair of human proteins acoording to their sequence amino acid constitution. should I blast these pairs(blast2seq) or align these pairs(localAlignment)?

Answer 1

[5heikki]

I'd go for global alignments since the majority of eukaryote proteins consist of the same domains in different orders..