1. Local alignment and BLAST Usman Roshan BNFO 601

2. Local alignment Global alignment recursions: Local alignment recursions

3. Local alignment traceback Let T(i,j) be the traceback matrices and m and n be length of input sequences. Global alignment traceback: –Begin from T(m,n) and stop at T(0,0). Local alignment traceback: –Find i *,j * such that T(i *,j * ) is the maximum over all T(i,j). –Begin traceback from T(i *,j * ) and stop when T(i,j) <= 0.

4. BLAST Local pairwise alignment heuristic Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive. Online server: http://www.ncbi.nlm.nih.gov/blast http://www.ncbi.nlm.nih.gov/blast

5. BLAST 1.Given a query q and a target sequence, find substrings of length k (k-mers) of score at least t --- also called hits. k is normally 3 to 5 for amino acids and 12 for nucleotides. 2.Extend each hit to a locally maximal segment. Terminate the extension when the reduction in score exceeds a pre-defined threshold 3.Report maximal segments above score S.

6. Finding k-mers quickly Preprocess the database of sequences: –For each sequence in the database store all k-mers in hash-table. –This takes linear time Query sequence: –For each k-mer in the query sequence look up the hash table of the target to see if it exists –Also takes linear time