| | Re: homology search
It depends of what you need to compare. If you want to do a comparison of a single sequence against a sequence database in order to find if it shares conserved region (domain) with another sequences you have to use PSI-BLAST. The algorithm will include your sequence (or part of it) in a position-specific scoring matrix and will continue searching the database for new matches with the generated PSSM. If you want to find out a specific domain in your sequence, then use PHHMER - the algorithm will compare your FASTA sequence to a HMMPfam database which is an excellent collection of precalculated Hidden Markov Models of well annotated functional domains.