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Sequence Similarity Searching
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  Sequence Similarity Searching    Why Compare Sequences?   ã Identify sequences found in lab experiments ã  What is this thing I just found? ã Compare new genes to known ones ã Compare genes from different species ã  information about evolution ã Guess functions for entire genomes full of new gene sequences  Alignments tell us about...* ã Function or activity of a new gene/protein ã Structure or shape of a new protein ã Location or preferred location of a protein ã Stability of a gene or protein ã Origin of a gene or protein ã Origin or phylogeny of an organelle ã Origin or phylogeny of an organism  Are there other sequences like this one? ã Sequence comparison is the most powerful and reliable method to determine evolutionary relationships between genes ã Similarity searching is based on alignment ã BLAST  and FASTA  provide rapid similarity searching  –  a. rapid = approximate (heuristic)  –   b. false + and - scores
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